Kasper Daniel Hansen authored on 31/10/2025 15:03:21
A Wokaty authored on 29/10/2025 14:11:31
A Wokaty authored on 29/10/2025 14:11:31
Kasper Daniel Hansen authored on 10/10/2025 15:22:10
Kasper Daniel Hansen authored on 04/10/2025 15:07:28
Hervé Pagès authored on 21/06/2025 23:32:56
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.45.1 |
|
| 2 |
+Version: 1.45.2 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store whole-genome methylation data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing whole-genome |
| ... | ... |
@@ -18,7 +18,7 @@ Depends: |
| 18 | 18 |
SummarizedExperiment (>= 1.19.5) |
| 19 | 19 |
Imports: |
| 20 | 20 |
IRanges (>= 2.23.9), |
| 21 |
- GenomeInfoDb, |
|
| 21 |
+ Seqinfo, |
|
| 22 | 22 |
scales, |
| 23 | 23 |
stats, |
| 24 | 24 |
parallel, |
SrenBlikdal authored on 29/04/2025 19:12:51
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.45.0 |
|
| 2 |
+Version: 1.45.1 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store whole-genome methylation data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing whole-genome |
| ... | ... |
@@ -61,6 +61,7 @@ Collate: |
| 61 | 61 |
BSseq_utils.R |
| 62 | 62 |
combine.R |
| 63 | 63 |
read.bismark.R |
| 64 |
+ read.bedMethyl.R |
|
| 64 | 65 |
read.modbam2bed.R |
| 65 | 66 |
read.modkit.R |
| 66 | 67 |
BSmooth.R |
| ... | ... |
@@ -79,6 +80,7 @@ Collate: |
| 79 | 80 |
FWIRanges-class.R |
| 80 | 81 |
FWGRanges-class.R |
| 81 | 82 |
findLoci.R |
| 83 |
+ Likelihood_functions.R |
|
| 82 | 84 |
License: Artistic-2.0 |
| 83 | 85 |
VignetteBuilder: knitr |
| 84 | 86 |
URL: https://github.com/kasperdanielhansen/bsseq |
A Wokaty authored on 15/04/2025 14:14:33
A Wokaty authored on 15/04/2025 14:14:33
Peter Hickey authored on 16/12/2024 04:17:52
Peter Hickey authored on 16/12/2024 04:17:48
| ... | ... |
@@ -7,7 +7,9 @@ Description: A collection of tools for analyzing and visualizing whole-genome |
| 7 | 7 |
sequencing and Oxford nanopore data. |
| 8 | 8 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
| 9 | 9 |
email = "[email protected]", comment = c(ORCID = "0000-0003-0086-0687")), |
| 10 |
- person("Peter", "Hickey", role = "aut", email = "[email protected]"))
|
|
| 10 |
+ person("Peter", "Hickey", role = "aut", email = "[email protected]", comment = c(ORCID = "0000-0002-8153-6258")),
|
|
| 11 |
+ person("Hervé", "Pagès", role = "ctb"),
|
|
| 12 |
+ person("Aaron", "Lun", role = "ctb"))
|
|
| 11 | 13 |
Depends: |
| 12 | 14 |
R (>= 4.0), |
| 13 | 15 |
methods, |
LTLA authored on 27/11/2024 04:13:23
LTLA authored on 25/11/2024 01:44:16
LTLA authored on 24/11/2024 23:06:46
| ... | ... |
@@ -38,7 +38,8 @@ Imports: |
| 38 | 38 |
Biostrings, |
| 39 | 39 |
utils, |
| 40 | 40 |
HDF5Array (>= 1.19.11), |
| 41 |
- rhdf5 |
|
| 41 |
+ rhdf5, |
|
| 42 |
+ beachmat |
|
| 42 | 43 |
Suggests: |
| 43 | 44 |
testthat, |
| 44 | 45 |
bsseqData, |
| ... | ... |
@@ -49,7 +50,6 @@ Suggests: |
| 49 | 50 |
doParallel, |
| 50 | 51 |
rtracklayer, |
| 51 | 52 |
BSgenome.Hsapiens.UCSC.hg38, |
| 52 |
- beachmat (>= 1.5.2), |
|
| 53 | 53 |
batchtools |
| 54 | 54 |
Collate: |
| 55 | 55 |
utils.R |
| ... | ... |
@@ -82,6 +82,10 @@ VignetteBuilder: knitr |
| 82 | 82 |
URL: https://github.com/kasperdanielhansen/bsseq |
| 83 | 83 |
BugReports: https://github.com/kasperdanielhansen/bsseq/issues |
| 84 | 84 |
biocViews: DNAMethylation |
| 85 |
-LinkingTo: Rcpp, beachmat |
|
| 85 |
+LinkingTo: |
|
| 86 |
+ Rcpp, |
|
| 87 |
+ beachmat, |
|
| 88 |
+ assorthead |
|
| 89 |
+SystemRequirements: C++17 |
|
| 86 | 90 |
NeedsCompilation: yes |
| 87 | 91 |
RoxygenNote: 7.1.0 |
J Wokaty authored on 29/10/2024 13:41:53
J Wokaty authored on 29/10/2024 13:41:53
Kasper Daniel Hansen authored on 17/10/2024 13:38:22
Kasper Daniel Hansen authored on 15/10/2024 22:12:55
J Wokaty authored on 30/04/2024 14:28:16
J Wokaty authored on 30/04/2024 14:28:16
Previous merge had the wrong version number
Kasper Daniel Hansen authored on 08/04/2024 18:42:42
• GitHub committed on 08/04/2024 18:42:42
yixuan-chen-elisa authored on 03/04/2024 21:09:06
Kasper Daniel Hansen authored on 29/03/2024 18:39:49
Kasper Daniel Hansen authored on 16/11/2023 02:06:37
• GitHub committed on 16/11/2023 02:06:37
yixuanchen authored on 15/11/2023 22:03:15
• GitHub committed on 15/11/2023 22:03:15
Kasper Daniel Hansen authored on 15/11/2023 21:16:00
| ... | ... |
@@ -1,11 +1,12 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.39.0 |
|
| 2 |
+Version: 1.39.1 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 |
-Title: Analyze, manage and store bisulfite sequencing data |
|
| 5 |
-Description: A collection of tools for analyzing and visualizing bisulfite |
|
| 6 |
- sequencing data. |
|
| 4 |
+Title: Analyze, manage and store whole-genome methylation data |
|
| 5 |
+Description: A collection of tools for analyzing and visualizing whole-genome |
|
| 6 |
+ methylation data from sequencing. This includes whole-genome bisulfite |
|
| 7 |
+ sequencing and Oxford nanopore data. |
|
| 7 | 8 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
| 8 |
- email = "[email protected]"), |
|
| 9 |
+ email = "[email protected]", comment = c(ORCID = "0000-0003-0086-0687")), |
|
| 9 | 10 |
person("Peter", "Hickey", role = "aut", email = "[email protected]"))
|
| 10 | 11 |
Depends: |
| 11 | 12 |
R (>= 4.0), |
| ... | ... |
@@ -18,6 +19,8 @@ Imports: |
| 18 | 19 |
GenomeInfoDb, |
| 19 | 20 |
scales, |
| 20 | 21 |
stats, |
| 22 |
+ parallel, |
|
| 23 |
+ tools, |
|
| 21 | 24 |
graphics, |
| 22 | 25 |
Biobase, |
| 23 | 26 |
locfit, |
| ... | ... |
@@ -55,7 +58,6 @@ Collate: |
| 55 | 58 |
BSseqTstat_class.R |
| 56 | 59 |
BSseq_utils.R |
| 57 | 60 |
combine.R |
| 58 |
- read.bsmooth.R |
|
| 59 | 61 |
read.bismark.R |
| 60 | 62 |
read.modbam2bed.R |
| 61 | 63 |
BSmooth.R |
yixuan-chen-elisa authored on 13/11/2023 21:01:06
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.39.0 |
|
| 2 |
+Version: 1.39.1 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -58,6 +58,7 @@ Collate: |
| 58 | 58 |
read.bsmooth.R |
| 59 | 59 |
read.bismark.R |
| 60 | 60 |
read.modbam2bed.R |
| 61 |
+ read.modkit.R |
|
| 61 | 62 |
BSmooth.R |
| 62 | 63 |
BSmooth.tstat.R |
| 63 | 64 |
dmrFinder.R |
Kasper Daniel Hansen authored on 01/11/2023 20:50:12
J Wokaty authored on 24/10/2023 13:50:39
J Wokaty authored on 24/10/2023 13:50:39
Kasper Daniel Hansen authored on 21/09/2023 14:39:37
Kasper Daniel Hansen authored on 21/09/2023 14:36:46
Kasper Daniel Hansen authored on 21/09/2023 14:36:40
J Wokaty authored on 25/04/2023 14:23:31
J Wokaty authored on 25/04/2023 14:23:31
Kasper Daniel Hansen authored on 23/04/2023 20:53:15
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.35.0 |
|
| 2 |
+Version: 1.35.1 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -47,7 +47,7 @@ Suggests: |
| 47 | 47 |
rtracklayer, |
| 48 | 48 |
BSgenome.Hsapiens.UCSC.hg38, |
| 49 | 49 |
beachmat (>= 1.5.2), |
| 50 |
- BatchJobs |
|
| 50 |
+ batchtools |
|
| 51 | 51 |
Collate: |
| 52 | 52 |
utils.R |
| 53 | 53 |
hasGRanges.R |
| ... | ... |
@@ -78,7 +78,6 @@ VignetteBuilder: knitr |
| 78 | 78 |
URL: https://github.com/kasperdanielhansen/bsseq |
| 79 | 79 |
BugReports: https://github.com/kasperdanielhansen/bsseq/issues |
| 80 | 80 |
biocViews: DNAMethylation |
| 81 |
-SystemRequirements: C++11 |
|
| 82 | 81 |
LinkingTo: Rcpp, beachmat |
| 83 | 82 |
NeedsCompilation: yes |
| 84 | 83 |
RoxygenNote: 7.1.0 |
J Wokaty authored on 01/11/2022 15:07:09
J Wokaty authored on 01/11/2022 15:07:09
Nitesh Turaga authored on 26/04/2022 15:11:30
Nitesh Turaga authored on 26/04/2022 15:11:30
&& is always preferred over & in if conditions as it prevents the
right operand of the && operation from being unnecessarily evaluated.
In this particular case this change preventively repairs the
updateObject() method for BSseq objects that will otherwise break
on objects with DataFrame instances in them when DataFrame becomes
a virtual class in the S4Vectors package (will happen soon).
Hervé Pagès authored on 02/11/2021 01:52:48
Nitesh Turaga authored on 26/10/2021 16:03:49
Nitesh Turaga authored on 26/10/2021 16:03:49
Nitesh Turaga authored on 19/05/2021 15:53:03
Nitesh Turaga authored on 19/05/2021 15:53:03
Hervé Pagès authored on 26/04/2021 05:55:03
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.27.4 |
|
| 2 |
+Version: 1.27.5 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -34,7 +34,7 @@ Imports: |
| 34 | 34 |
BSgenome, |
| 35 | 35 |
Biostrings, |
| 36 | 36 |
utils, |
| 37 |
- HDF5Array (>= 1.15.19), |
|
| 37 |
+ HDF5Array (>= 1.19.11), |
|
| 38 | 38 |
rhdf5 |
| 39 | 39 |
Suggests: |
| 40 | 40 |
testthat, |
The object was loaded and updated with updateObject(), and then
reserialized. This had the effect of replacing all DataFrame instances
contained in the object with DFrame instances.
Note that starting with S4Vectors 0.24.0, all DataFrame instances
should be replaced with DFrame instances.
Hervé Pagès authored on 06/04/2021 01:37:29
kasperdanielhansen authored on 23/03/2021 08:07:57
Kasper Daniel Hansen authored on 15/03/2021 23:01:13
kasperdanielhansen authored on 09/02/2021 09:35:19
Nitesh Turaga authored on 27/10/2020 14:46:25
Nitesh Turaga authored on 27/10/2020 14:46:25
Hervé Pagès authored on 09/10/2020 05:05:28
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.25.6 |
|
| 2 |
+Version: 1.25.7 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -28,7 +28,7 @@ Imports: |
| 28 | 28 |
DelayedMatrixStats (>= 1.5.2), |
| 29 | 29 |
permute, |
| 30 | 30 |
limma, |
| 31 |
- DelayedArray (>= 0.15.10), |
|
| 31 |
+ DelayedArray (>= 0.15.16), |
|
| 32 | 32 |
Rcpp, |
| 33 | 33 |
BiocParallel, |
| 34 | 34 |
BSgenome, |
Hervé Pagès authored on 27/09/2020 01:24:50
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.25.5 |
|
| 2 |
+Version: 1.25.6 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -28,7 +28,7 @@ Imports: |
| 28 | 28 |
DelayedMatrixStats (>= 1.5.2), |
| 29 | 29 |
permute, |
| 30 | 30 |
limma, |
| 31 |
- DelayedArray (>= 0.9.8), |
|
| 31 |
+ DelayedArray (>= 0.15.10), |
|
| 32 | 32 |
Rcpp, |
| 33 | 33 |
BiocParallel, |
| 34 | 34 |
BSgenome, |
Peter Hickey authored on 29/06/2020 01:21:07
Peter Hickey authored on 29/06/2020 01:21:02
| ... | ... |
@@ -8,7 +8,7 @@ Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
| 8 | 8 |
email = "[email protected]"), |
| 9 | 9 |
person("Peter", "Hickey", role = "aut", email = "[email protected]"))
|
| 10 | 10 |
Depends: |
| 11 |
- R (>= 3.5), |
|
| 11 |
+ R (>= 4.0), |
|
| 12 | 12 |
methods, |
| 13 | 13 |
BiocGenerics, |
| 14 | 14 |
GenomicRanges (>= 1.41.5), |
| ... | ... |
@@ -34,7 +34,7 @@ Imports: |
| 34 | 34 |
BSgenome, |
| 35 | 35 |
Biostrings, |
| 36 | 36 |
utils, |
| 37 |
- HDF5Array (>= 1.11.9), |
|
| 37 |
+ HDF5Array (>= 1.15.19), |
|
| 38 | 38 |
rhdf5 |
| 39 | 39 |
Suggests: |
| 40 | 40 |
testthat, |
Hervé Pagès authored on 09/06/2020 01:36:15
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.25.3 |
|
| 2 |
+Version: 1.25.4 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -11,10 +11,10 @@ Depends: |
| 11 | 11 |
R (>= 3.5), |
| 12 | 12 |
methods, |
| 13 | 13 |
BiocGenerics, |
| 14 |
- GenomicRanges (>= 1.33.6), |
|
| 15 |
- SummarizedExperiment (>= 1.17.4) |
|
| 14 |
+ GenomicRanges (>= 1.41.5), |
|
| 15 |
+ SummarizedExperiment (>= 1.19.5) |
|
| 16 | 16 |
Imports: |
| 17 |
- IRanges (>= 2.23.5), |
|
| 17 |
+ IRanges (>= 2.23.9), |
|
| 18 | 18 |
GenomeInfoDb, |
| 19 | 19 |
scales, |
| 20 | 20 |
stats, |
| ... | ... |
@@ -23,7 +23,7 @@ Imports: |
| 23 | 23 |
locfit, |
| 24 | 24 |
gtools, |
| 25 | 25 |
data.table (>= 1.11.8), |
| 26 |
- S4Vectors (>= 0.25.14), |
|
| 26 |
+ S4Vectors (>= 0.27.12), |
|
| 27 | 27 |
R.utils (>= 2.0.0), |
| 28 | 28 |
DelayedMatrixStats (>= 1.5.2), |
| 29 | 29 |
permute, |
Peter Hickey authored on 04/06/2020 03:06:29
Peter Hickey authored on 01/06/2020 09:36:15
Also add overlapsAny() methods and improve granges() method for
hasGRanges derivatives.
Hervé Pagès authored on 20/05/2020 22:23:58
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.25.0 |
|
| 2 |
+Version: 1.25.1 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -14,7 +14,7 @@ Depends: |
| 14 | 14 |
GenomicRanges (>= 1.33.6), |
| 15 | 15 |
SummarizedExperiment (>= 1.17.4) |
| 16 | 16 |
Imports: |
| 17 |
- IRanges (>= 2.21.6), |
|
| 17 |
+ IRanges (>= 2.23.5), |
|
| 18 | 18 |
GenomeInfoDb, |
| 19 | 19 |
scales, |
| 20 | 20 |
stats, |
Nitesh Turaga authored on 27/04/2020 18:30:19
Nitesh Turaga authored on 27/04/2020 18:30:19
Peter Hickey authored on 24/04/2020 04:34:15
PeteHaitch authored on 24/04/2020 03:23:25
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.23.2 |
|
| 2 |
+Version: 1.23.3 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -81,4 +81,4 @@ biocViews: DNAMethylation |
| 81 | 81 |
SystemRequirements: C++11 |
| 82 | 82 |
LinkingTo: Rcpp, beachmat |
| 83 | 83 |
NeedsCompilation: yes |
| 84 |
-RoxygenNote: 6.1.0 |
|
| 84 |
+RoxygenNote: 7.1.0 |
kasperdanielhansen authored on 06/04/2020 16:21:59
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.23.1 |
|
| 2 |
+Version: 1.23.2 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -76,8 +76,6 @@ Collate: |
| 76 | 76 |
License: Artistic-2.0 |
| 77 | 77 |
VignetteBuilder: knitr |
| 78 | 78 |
URL: https://github.com/kasperdanielhansen/bsseq |
| 79 |
-LazyData: yes |
|
| 80 |
-LazyDataCompression: xz |
|
| 81 | 79 |
BugReports: https://github.com/kasperdanielhansen/bsseq/issues |
| 82 | 80 |
biocViews: DNAMethylation |
| 83 | 81 |
SystemRequirements: C++11 |
Hervé Pagès authored on 24/03/2020 06:15:16
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.23.0 |
|
| 2 |
+Version: 1.23.1 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -11,10 +11,10 @@ Depends: |
| 11 | 11 |
R (>= 3.5), |
| 12 | 12 |
methods, |
| 13 | 13 |
BiocGenerics, |
| 14 |
- GenomicRanges (>= 1.29.14), |
|
| 15 |
- SummarizedExperiment (>= 1.9.18) |
|
| 14 |
+ GenomicRanges (>= 1.33.6), |
|
| 15 |
+ SummarizedExperiment (>= 1.17.4) |
|
| 16 | 16 |
Imports: |
| 17 |
- IRanges (>= 2.11.16), |
|
| 17 |
+ IRanges (>= 2.21.6), |
|
| 18 | 18 |
GenomeInfoDb, |
| 19 | 19 |
scales, |
| 20 | 20 |
stats, |
| ... | ... |
@@ -23,7 +23,7 @@ Imports: |
| 23 | 23 |
locfit, |
| 24 | 24 |
gtools, |
| 25 | 25 |
data.table (>= 1.11.8), |
| 26 |
- S4Vectors (>= 0.23.11), |
|
| 26 |
+ S4Vectors (>= 0.25.14), |
|
| 27 | 27 |
R.utils (>= 2.0.0), |
| 28 | 28 |
DelayedMatrixStats (>= 1.5.2), |
| 29 | 29 |
permute, |
Nitesh Turaga authored on 29/10/2019 17:36:17
Nitesh Turaga authored on 29/10/2019 17:08:33
Hervé Pagès authored on 12/06/2019 15:24:37
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.21.0 |
|
| 2 |
+Version: 1.21.1 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -23,7 +23,7 @@ Imports: |
| 23 | 23 |
locfit, |
| 24 | 24 |
gtools, |
| 25 | 25 |
data.table (>= 1.11.8), |
| 26 |
- S4Vectors, |
|
| 26 |
+ S4Vectors (>= 0.23.11), |
|
| 27 | 27 |
R.utils (>= 2.0.0), |
| 28 | 28 |
DelayedMatrixStats (>= 1.5.2), |
| 29 | 29 |
permute, |
Nitesh Turaga authored on 02/05/2019 16:11:13
Nitesh Turaga authored on 02/05/2019 15:53:37
Peter Hickey authored on 23/04/2019 02:34:09
Peter Hickey authored on 23/04/2019 01:24:19
Peter Hickey authored on 23/04/2019 01:04:08
Peter Hickey authored on 23/04/2019 01:03:45
| ... | ... |
@@ -81,6 +81,6 @@ LazyDataCompression: xz |
| 81 | 81 |
BugReports: https://github.com/kasperdanielhansen/bsseq/issues |
| 82 | 82 |
biocViews: DNAMethylation |
| 83 | 83 |
SystemRequirements: C++11 |
| 84 |
-LinkingTo: Rcpp, Rhdf5lib, beachmat |
|
| 84 |
+LinkingTo: Rcpp, beachmat |
|
| 85 | 85 |
NeedsCompilation: yes |
| 86 | 86 |
RoxygenNote: 6.1.0 |
Hervé Pagès authored on 31/01/2019 22:38:18
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.19.2 |
|
| 2 |
+Version: 1.19.3 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -25,10 +25,10 @@ Imports: |
| 25 | 25 |
data.table (>= 1.11.8), |
| 26 | 26 |
S4Vectors, |
| 27 | 27 |
R.utils (>= 2.0.0), |
| 28 |
- DelayedMatrixStats (>= 1.3.6), |
|
| 28 |
+ DelayedMatrixStats (>= 1.5.2), |
|
| 29 | 29 |
permute, |
| 30 | 30 |
limma, |
| 31 |
- DelayedArray (>= 0.7.15), |
|
| 31 |
+ DelayedArray (>= 0.9.8), |
|
| 32 | 32 |
Rcpp, |
| 33 | 33 |
BiocParallel, |
| 34 | 34 |
BSgenome, |
Peter Hickey authored on 15/01/2019 05:58:24
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.19.1 |
|
| 2 |
+Version: 1.19.2 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -46,7 +46,7 @@ Suggests: |
| 46 | 46 |
doParallel, |
| 47 | 47 |
rtracklayer, |
| 48 | 48 |
BSgenome.Hsapiens.UCSC.hg38, |
| 49 |
- beachmat, |
|
| 49 |
+ beachmat (>= 1.5.2), |
|
| 50 | 50 |
BatchJobs |
| 51 | 51 |
Collate: |
| 52 | 52 |
utils.R |
Peter Hickey authored on 15/01/2019 05:55:22
Hervé Pagès authored on 13/12/2018 20:18:12
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.19.0 |
|
| 2 |
+Version: 1.19.1 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -34,7 +34,7 @@ Imports: |
| 34 | 34 |
BSgenome, |
| 35 | 35 |
Biostrings, |
| 36 | 36 |
utils, |
| 37 |
- HDF5Array, |
|
| 37 |
+ HDF5Array (>= 1.11.9), |
|
| 38 | 38 |
rhdf5 |
| 39 | 39 |
Suggests: |
| 40 | 40 |
testthat, |
Peter Hickey authored on 30/10/2018 20:40:12
vobencha authored on 30/10/2018 15:54:30
vobencha authored on 30/10/2018 15:41:49
Kasper Daniel Hansen authored on 30/10/2018 02:51:14
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.17.8 |
|
| 2 |
+Version: 1.17.9 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -46,7 +46,8 @@ Suggests: |
| 46 | 46 |
doParallel, |
| 47 | 47 |
rtracklayer, |
| 48 | 48 |
BSgenome.Hsapiens.UCSC.hg38, |
| 49 |
- beachmat |
|
| 49 |
+ beachmat, |
|
| 50 |
+ BatchJobs |
|
| 50 | 51 |
Collate: |
| 51 | 52 |
utils.R |
| 52 | 53 |
hasGRanges.R |
Kasper Daniel Hansen authored on 30/10/2018 00:57:46
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.17.7 |
|
| 2 |
+Version: 1.17.8 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -35,7 +35,7 @@ Imports: |
| 35 | 35 |
Biostrings, |
| 36 | 36 |
utils, |
| 37 | 37 |
HDF5Array, |
| 38 |
- beachmat |
|
| 38 |
+ rhdf5 |
|
| 39 | 39 |
Suggests: |
| 40 | 40 |
testthat, |
| 41 | 41 |
bsseqData, |
| ... | ... |
@@ -45,7 +45,8 @@ Suggests: |
| 45 | 45 |
Matrix, |
| 46 | 46 |
doParallel, |
| 47 | 47 |
rtracklayer, |
| 48 |
- BSgenome.Hsapiens.UCSC.hg38 |
|
| 48 |
+ BSgenome.Hsapiens.UCSC.hg38, |
|
| 49 |
+ beachmat |
|
| 49 | 50 |
Collate: |
| 50 | 51 |
utils.R |
| 51 | 52 |
hasGRanges.R |
Peter Hickey authored on 24/10/2018 20:21:55
- Small tweak to default @trans function in BSseq() and combine().
- Add unit test
Peter Hickey authored on 15/10/2018 05:04:53
Peter Hickey authored on 14/10/2018 22:45:48
- Now uses fread()'s native support of compressed files
- Supports fread()'s nThreads argument
Peter Hickey authored on 07/10/2018 03:37:11
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.17.3 |
|
| 2 |
+Version: 1.17.4 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -22,7 +22,7 @@ Imports: |
| 22 | 22 |
Biobase, |
| 23 | 23 |
locfit, |
| 24 | 24 |
gtools, |
| 25 |
- data.table, |
|
| 25 |
+ data.table (>= 1.11.8), |
|
| 26 | 26 |
S4Vectors, |
| 27 | 27 |
R.utils (>= 2.0.0), |
| 28 | 28 |
DelayedMatrixStats (>= 1.3.6), |
Peter Hickey authored on 17/09/2018 11:47:23
Peter Hickey authored on 17/09/2018 11:17:52
Peter Hickey authored on 17/09/2018 11:08:03
Peter Hickey authored on 17/09/2018 11:02:52
LiNk-NY authored on 07/09/2018 18:03:11
LiNk-NY authored on 30/08/2018 17:45:52
Peter Hickey authored on 21/08/2018 03:47:21
| ... | ... |
@@ -25,7 +25,7 @@ Imports: |
| 25 | 25 |
data.table, |
| 26 | 26 |
S4Vectors, |
| 27 | 27 |
R.utils (>= 2.0.0), |
| 28 |
- DelayedMatrixStats (>= 1.3.4), |
|
| 28 |
+ DelayedMatrixStats (>= 1.3.6), |
|
| 29 | 29 |
permute, |
| 30 | 30 |
limma, |
| 31 | 31 |
DelayedArray (>= 0.7.15), |
| ... | ... |
@@ -79,3 +79,4 @@ biocViews: DNAMethylation |
| 79 | 79 |
SystemRequirements: C++11 |
| 80 | 80 |
LinkingTo: Rcpp, Rhdf5lib, beachmat |
| 81 | 81 |
NeedsCompilation: yes |
| 82 |
+RoxygenNote: 6.1.0 |
Found that `readr::read_tsv()` was painfully slow for large gzipped Bismark files (e.g., mCH loci).
Instead, now use:
- If file is gzipped and `gzip` is available at the command line, then use `data.table::fread()`.
- If file is gzipped and `gzip` is **not** available at the command line, then use `utils::read.table()`.
- If file is not gzipped (plain text) use `data.table::fread()`.
There are still some kinks to work out and tradeoffs to explore.
Peter Hickey authored on 04/07/2018 02:41:15
Peter Hickey authored on 29/06/2018 14:30:47
Peter Hickey authored on 28/06/2018 16:03:26
- HDF5Array and beachmat in Imports rather than Suggests
Peter Hickey authored on 14/06/2018 20:43:20
| ... | ... |
@@ -8,7 +8,7 @@ Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
| 8 | 8 |
email = "[email protected]"), |
| 9 | 9 |
person("Peter", "Hickey", role = "aut", email = "[email protected]"))
|
| 10 | 10 |
Depends: |
| 11 |
- R (>= 3.3), |
|
| 11 |
+ R (>= 3.5), |
|
| 12 | 12 |
methods, |
| 13 | 13 |
BiocGenerics, |
| 14 | 14 |
GenomicRanges (>= 1.29.14), |
| ... | ... |
@@ -25,25 +25,25 @@ Imports: |
| 25 | 25 |
data.table, |
| 26 | 26 |
S4Vectors, |
| 27 | 27 |
R.utils (>= 2.0.0), |
| 28 |
- DelayedMatrixStats (>= 1.1.12), |
|
| 28 |
+ DelayedMatrixStats (>= 1.3.1), |
|
| 29 | 29 |
permute, |
| 30 | 30 |
limma, |
| 31 |
- DelayedArray (>= 0.5.34), |
|
| 31 |
+ DelayedArray (>= 0.7.6), |
|
| 32 | 32 |
Rcpp, |
| 33 | 33 |
BiocParallel, |
| 34 | 34 |
readr, |
| 35 | 35 |
BSgenome, |
| 36 | 36 |
Biostrings, |
| 37 |
- utils |
|
| 37 |
+ utils, |
|
| 38 |
+ HDF5Array, |
|
| 39 |
+ beachmat |
|
| 38 | 40 |
Suggests: |
| 39 | 41 |
testthat, |
| 40 | 42 |
bsseqData, |
| 41 | 43 |
BiocStyle, |
| 42 | 44 |
rmarkdown, |
| 43 | 45 |
knitr, |
| 44 |
- beachmat, |
|
| 45 | 46 |
Matrix, |
| 46 |
- HDF5Array, |
|
| 47 | 47 |
doParallel |
| 48 | 48 |
Collate: |
| 49 | 49 |
utils.R |
Peter Hickey authored on 14/06/2018 19:39:15
- Make generic with methods for _BSgenome_ and _DNAStringSet_ (e.g., a FASTA file imported with `rtracklayer::import()`)
Peter Hickey authored on 13/06/2018 14:17:09
Peter Hickey authored on 12/06/2018 19:56:44
Peter Hickey authored on 10/06/2018 14:37:16
These are superseded by FWGRanges, which implement the correct strand-matching behaviour that is surprisingly difficult to achieve otherwise.
Long term, I'd like to support FWGRanges as the rowRanges in a BSseq object.
Peter Hickey authored on 05/06/2018 20:28:32
Peter Hickey authored on 05/06/2018 18:36:20
Slightly formalise intermediate objects lociDT and BSseqDT.
Split these out into their own files.
Refine construction of 'gr' from Bismark files.
Peter Hickey authored on 31/05/2018 19:23:24
Peter Hickey authored on 29/05/2018 12:56:37
- BSseq objects can once again use ordinary matrix objects as assays.
- Reimplement `BSmooth()` more-or-less from scratch:
- Switch from 'parallel' to 'BiocParallel' for parallelization. This brings some notable improvements:
- Smoothed results can now be written directly to an on-disk realization backend by the worker. This dramatically reduces memory usage compared to previous versions of 'bsseq' that required all results be retained in-memory.
- Parallelization is now supported on Windows through the use of a 'SnowParam' object as the value of `BPPARAM`.
- Improved error handling makes it possible to gracefully resume `BSmooth()` jobs that encountered errors by re-doing only the necessary tasks.
- Detailed and extensive job logging facilities.
- Fix bug in `BSmooth()` with the `maxGap` parameter.
- Re-factor BSseq() constructor and add fast, internal .BSseq() constructor.
- Re-factor collapseBSseq() and combine(). Should be much more performant.
- Use beachmat to implement fast validity checking of 'M' and 'Cov' matrices.
- Resave BS.chr22 (supplied data) using integer for storage mode of assays to reduce size.
- Switch from RUnit to testthat. testthat has better integration with code coverage tools that help when refactoring.
Peter Hickey authored on 28/05/2018 23:42:18
| ... | ... |
@@ -12,8 +12,7 @@ Depends: |
| 12 | 12 |
methods, |
| 13 | 13 |
BiocGenerics, |
| 14 | 14 |
GenomicRanges (>= 1.29.14), |
| 15 |
- SummarizedExperiment (>= 1.9.18), |
|
| 16 |
- parallel |
|
| 15 |
+ SummarizedExperiment (>= 1.9.18) |
|
| 17 | 16 |
Imports: |
| 18 | 17 |
IRanges (>= 2.11.16), |
| 19 | 18 |
GenomeInfoDb, |
| ... | ... |
@@ -30,17 +29,24 @@ Imports: |
| 30 | 29 |
permute, |
| 31 | 30 |
limma, |
| 32 | 31 |
DelayedArray (>= 0.5.34), |
| 33 |
- HDF5Array |
|
| 32 |
+ Rcpp, |
|
| 33 |
+ BiocParallel, |
|
| 34 |
+ readr |
|
| 34 | 35 |
Suggests: |
| 35 |
- RUnit, |
|
| 36 |
+ testthat, |
|
| 36 | 37 |
bsseqData, |
| 37 | 38 |
BiocStyle, |
| 38 | 39 |
rmarkdown, |
| 39 | 40 |
knitr, |
| 41 |
+ beachmat, |
|
| 42 |
+ Matrix, |
|
| 43 |
+ HDF5Array, |
|
| 44 |
+ doParallel, |
|
| 45 |
+ testthat |
|
| 40 | 46 |
Collate: |
| 41 | 47 |
utils.R |
| 42 | 48 |
hasGRanges.R |
| 43 |
- BSseq_class.R |
|
| 49 |
+ BSseq-class.R |
|
| 44 | 50 |
BSseqTstat_class.R |
| 45 | 51 |
BSseq_utils.R |
| 46 | 52 |
combine.R |
| ... | ... |
@@ -57,8 +63,8 @@ Collate: |
| 57 | 63 |
BSseqStat_class.R |
| 58 | 64 |
getStats.R |
| 59 | 65 |
hdf5_utils.R |
| 60 |
- combine_utils.R |
|
| 61 | 66 |
DelayedArray_utils.R |
| 67 |
+ collapseBSseq.R |
|
| 62 | 68 |
License: Artistic-2.0 |
| 63 | 69 |
VignetteBuilder: knitr |
| 64 | 70 |
URL: https://github.com/kasperdanielhansen/bsseq |
| ... | ... |
@@ -66,3 +72,6 @@ LazyData: yes |
| 66 | 72 |
LazyDataCompression: xz |
| 67 | 73 |
BugReports: https://github.com/kasperdanielhansen/bsseq/issues |
| 68 | 74 |
biocViews: DNAMethylation |
| 75 |
+SystemRequirements: C++11 |
|
| 76 |
+LinkingTo: Rcpp, Rhdf5lib, beachmat |
|
| 77 |
+NeedsCompilation: yes |
Peter Hickey authored on 04/05/2018 18:31:03
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.17.0 |
|
| 2 |
+Version: 1.17.1 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -30,7 +30,8 @@ Imports: |
| 30 | 30 |
permute, |
| 31 | 31 |
limma, |
| 32 | 32 |
DelayedArray (>= 0.5.34), |
| 33 |
- HDF5Array |
|
| 33 |
+ HDF5Array, |
|
| 34 |
+ readr |
|
| 34 | 35 |
Suggests: |
| 35 | 36 |
RUnit, |
| 36 | 37 |
bsseqData, |
vobencha authored on 30/04/2018 14:41:38
vobencha authored on 30/04/2018 14:35:25
Peter Hickey authored on 27/04/2018 15:38:40
The method now calls the "updateObject" method for RangedSummarizedExperiment
objects (via callNextMethod()) early rather than late. The earlier the better
because very few things actually work in general on an outdated BSseq object
before that call is made. In particular the endoapply() loop that now follows
the call to callNextMethod() was failing if the BSseq object had "old"
DelayedArray objects in its assays.
Hervé Pagès authored on 27/04/2018 05:47:48
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.15.4 |
|
| 2 |
+Version: 1.15.5 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -12,7 +12,7 @@ Depends: |
| 12 | 12 |
methods, |
| 13 | 13 |
BiocGenerics, |
| 14 | 14 |
GenomicRanges (>= 1.29.14), |
| 15 |
- SummarizedExperiment (>= 1.7.8), |
|
| 15 |
+ SummarizedExperiment (>= 1.9.18), |
|
| 16 | 16 |
parallel |
| 17 | 17 |
Imports: |
| 18 | 18 |
IRanges (>= 2.11.16), |
| ... | ... |
@@ -29,7 +29,7 @@ Imports: |
| 29 | 29 |
DelayedMatrixStats (>= 1.1.12), |
| 30 | 30 |
permute, |
| 31 | 31 |
limma, |
| 32 |
- DelayedArray (>= 0.5.27), |
|
| 32 |
+ DelayedArray (>= 0.5.34), |
|
| 33 | 33 |
HDF5Array |
| 34 | 34 |
Suggests: |
| 35 | 35 |
RUnit, |
Peter Hickey authored on 24/04/2018 18:55:36
| ... | ... |
@@ -29,14 +29,14 @@ Imports: |
| 29 | 29 |
DelayedMatrixStats (>= 1.1.12), |
| 30 | 30 |
permute, |
| 31 | 31 |
limma, |
| 32 |
- DelayedArray (>= 0.5.27) |
|
| 32 |
+ DelayedArray (>= 0.5.27), |
|
| 33 |
+ HDF5Array |
|
| 33 | 34 |
Suggests: |
| 34 | 35 |
RUnit, |
| 35 | 36 |
bsseqData, |
| 36 | 37 |
BiocStyle, |
| 37 | 38 |
rmarkdown, |
| 38 | 39 |
knitr, |
| 39 |
- HDF5Array |
|
| 40 | 40 |
Collate: |
| 41 | 41 |
utils.R |
| 42 | 42 |
hasGRanges.R |
Peter Hickey authored on 24/04/2018 18:35:01
| ... | ... |
@@ -29,14 +29,14 @@ Imports: |
| 29 | 29 |
DelayedMatrixStats (>= 1.1.12), |
| 30 | 30 |
permute, |
| 31 | 31 |
limma, |
| 32 |
- DelayedArray (>= 0.5.27), |
|
| 33 |
- HDF5Array |
|
| 32 |
+ DelayedArray (>= 0.5.27) |
|
| 34 | 33 |
Suggests: |
| 35 | 34 |
RUnit, |
| 36 | 35 |
bsseqData, |
| 37 | 36 |
BiocStyle, |
| 38 | 37 |
rmarkdown, |
| 39 | 38 |
knitr, |
| 39 |
+ HDF5Array |
|
| 40 | 40 |
Collate: |
| 41 | 41 |
utils.R |
| 42 | 42 |
hasGRanges.R |
This is a straight find and replace of (col|row)(Sums|Means) with DelayedMatrixStats equivalents. Immediately, this is to work around an apparent bug in DelayedArray,rowSums-method (https://github.com/Bioconductor/DelayedArray/issues/16) but long term want to be using the optimised implementations in DelayedMatrixStat (e.g., using `cols` and `rows` args).
Peter Hickey authored on 24/04/2018 17:53:48
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.15.3 |
|
| 2 |
+Version: 1.15.4 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -26,7 +26,7 @@ Imports: |
| 26 | 26 |
data.table, |
| 27 | 27 |
S4Vectors, |
| 28 | 28 |
R.utils (>= 2.0.0), |
| 29 |
- matrixStats (>= 0.50.0), |
|
| 29 |
+ DelayedMatrixStats (>= 1.1.12), |
|
| 30 | 30 |
permute, |
| 31 | 31 |
limma, |
| 32 | 32 |
DelayedArray (>= 0.5.27), |
Peter Hickey authored on 17/04/2018 16:30:05
Update BS.chr22 assays (to use new DelayedArray internal representation) and rowRanges, and re-serialize it.
Peter Hickey authored on 08/04/2018 19:57:58
Peter Hickey authored on 08/04/2018 19:10:33
Peter Hickey authored on 08/04/2018 18:47:50
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.13.9 |
|
| 2 |
+Version: 1.13.10 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -29,7 +29,7 @@ Imports: |
| 29 | 29 |
matrixStats (>= 0.50.0), |
| 30 | 30 |
permute, |
| 31 | 31 |
limma, |
| 32 |
- DelayedArray, |
|
| 32 |
+ DelayedArray (>= 0.5.27), |
|
| 33 | 33 |
HDF5Array |
| 34 | 34 |
Suggests: |
| 35 | 35 |
RUnit, |
Hervé Pagès authored on 11/01/2018 07:51:59
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.15.0 |
|
| 2 |
+Version: 1.15.1 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -29,7 +29,7 @@ Imports: |
| 29 | 29 |
matrixStats (>= 0.50.0), |
| 30 | 30 |
permute, |
| 31 | 31 |
limma, |
| 32 |
- DelayedArray, |
|
| 32 |
+ DelayedArray (>= 0.5.16), |
|
| 33 | 33 |
HDF5Array |
| 34 | 34 |
Suggests: |
| 35 | 35 |
RUnit, |
Hervé Pagès authored on 30/10/2017 16:52:20
Hervé Pagès authored on 30/10/2017 16:39:45
Kasper Daniel Hansen authored on 17/10/2017 02:21:38
Kasper Daniel Hansen authored on 17/10/2017 02:21:02
Kasper Daniel Hansen authored on 16/10/2017 18:54:12
Hervé Pagès authored on 18/09/2017 15:02:27
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.13.6 |
|
| 2 |
+Version: 1.13.7 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -11,11 +11,11 @@ Depends: |
| 11 | 11 |
R (>= 3.3), |
| 12 | 12 |
methods, |
| 13 | 13 |
BiocGenerics, |
| 14 |
- GenomicRanges (>= 1.23.7), |
|
| 15 |
- SummarizedExperiment (>= 0.1.1), |
|
| 14 |
+ GenomicRanges (>= 1.29.14), |
|
| 15 |
+ SummarizedExperiment (>= 1.7.8), |
|
| 16 | 16 |
parallel |
| 17 | 17 |
Imports: |
| 18 |
- IRanges (>= 2.5.17), |
|
| 18 |
+ IRanges (>= 2.11.16), |
|
| 19 | 19 |
GenomeInfoDb, |
| 20 | 20 |
scales, |
| 21 | 21 |
stats, |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@131465 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 21/07/2017 12:17:16
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@130713 bc3139a8-67e5-0310-9ffc-ced21a209358
Herve Pages authored on 27/06/2017 17:05:27
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@129436 bc3139a8-67e5-0310-9ffc-ced21a209358
Herve Pages authored on 06/05/2017 06:23:15
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@129282 bc3139a8-67e5-0310-9ffc-ced21a209358
Herve Pages authored on 29/04/2017 20:29:37
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@129129 bc3139a8-67e5-0310-9ffc-ced21a209358
Herve Pages authored on 24/04/2017 19:50:57
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@129126 bc3139a8-67e5-0310-9ffc-ced21a209358
Herve Pages authored on 24/04/2017 19:25:24
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@128540 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 11/04/2017 13:48:47
| ... | ... |
@@ -1,19 +1,19 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.11.0 |
|
| 2 |
+Version: 1.11.2 |
|
| 3 |
+Encoding: UTF-8 |
|
| 3 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| 5 | 6 |
sequencing data. |
| 6 | 7 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
| 7 | 8 |
email = "[email protected]"), |
| 8 |
- person("Peter", "Hickey", role = "ctb", email = "[email protected]"))
|
|
| 9 |
+ person("Peter", "Hickey", role = "aut", email = "[email protected]"))
|
|
| 9 | 10 |
Depends: |
| 10 | 11 |
R (>= 3.3), |
| 11 | 12 |
methods, |
| 12 | 13 |
BiocGenerics, |
| 13 | 14 |
GenomicRanges (>= 1.23.7), |
| 14 | 15 |
SummarizedExperiment (>= 0.1.1), |
| 15 |
- parallel, |
|
| 16 |
- limma |
|
| 16 |
+ parallel |
|
| 17 | 17 |
Imports: |
| 18 | 18 |
IRanges (>= 2.5.17), |
| 19 | 19 |
GenomeInfoDb, |
| ... | ... |
@@ -27,19 +27,22 @@ Imports: |
| 27 | 27 |
S4Vectors, |
| 28 | 28 |
R.utils (>= 2.0.0), |
| 29 | 29 |
matrixStats (>= 0.50.0), |
| 30 |
- permute |
|
| 30 |
+ permute, |
|
| 31 |
+ limma, |
|
| 32 |
+ DelayedArray, |
|
| 33 |
+ HDF5Array |
|
| 31 | 34 |
Suggests: |
| 32 | 35 |
RUnit, |
| 33 | 36 |
bsseqData, |
| 34 | 37 |
BiocStyle, |
| 35 |
- knitr |
|
| 38 |
+ knitr, |
|
| 36 | 39 |
Collate: |
| 40 |
+ utils.R |
|
| 37 | 41 |
hasGRanges.R |
| 38 | 42 |
BSseq_class.R |
| 39 | 43 |
BSseqTstat_class.R |
| 40 | 44 |
BSseq_utils.R |
| 41 | 45 |
combine.R |
| 42 |
- utils.R |
|
| 43 | 46 |
read.bsmooth.R |
| 44 | 47 |
read.bismark.R |
| 45 | 48 |
BSmooth.R |
| ... | ... |
@@ -52,6 +55,9 @@ Collate: |
| 52 | 55 |
BSmooth.fstat.R |
| 53 | 56 |
BSseqStat_class.R |
| 54 | 57 |
getStats.R |
| 58 |
+ hdf5_utils.R |
|
| 59 |
+ combine_utils.R |
|
| 60 |
+ DelayedArray_utils.R |
|
| 55 | 61 |
License: Artistic-2.0 |
| 56 | 62 |
VignetteBuilder: knitr |
| 57 | 63 |
URL: https://github.com/kasperdanielhansen/bsseq |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@122712 bc3139a8-67e5-0310-9ffc-ced21a209358
Herve Pages authored on 17/10/2016 19:10:43
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@122710 bc3139a8-67e5-0310-9ffc-ced21a209358
Herve Pages authored on 17/10/2016 18:45:06
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@117512 bc3139a8-67e5-0310-9ffc-ced21a209358
Dan Tenenbaum authored on 15/05/2016 20:14:22
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@117323 bc3139a8-67e5-0310-9ffc-ced21a209358
Dan Tenenbaum authored on 11/05/2016 23:05:31
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@117081 bc3139a8-67e5-0310-9ffc-ced21a209358
Dan Tenenbaum authored on 03/05/2016 21:30:44
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@117079 bc3139a8-67e5-0310-9ffc-ced21a209358
Dan Tenenbaum authored on 03/05/2016 21:20:18
From: Kasper Daniel Hansen <[email protected]>
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@116910 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 29/04/2016 04:18:31
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.7.7 |
|
| 2 |
+Version: 1.7.13 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| 5 | 5 |
sequencing data. |
| ... | ... |
@@ -7,7 +7,7 @@ Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
| 7 | 7 |
email = "[email protected]"), |
| 8 | 8 |
person("Peter", "Hickey", role = "ctb", email = "[email protected]"))
|
| 9 | 9 |
Depends: |
| 10 |
- R (>= 2.15), |
|
| 10 |
+ R (>= 3.3), |
|
| 11 | 11 |
methods, |
| 12 | 12 |
BiocGenerics, |
| 13 | 13 |
GenomicRanges (>= 1.23.7), |
| ... | ... |
@@ -26,7 +26,7 @@ Imports: |
| 26 | 26 |
data.table, |
| 27 | 27 |
S4Vectors, |
| 28 | 28 |
R.utils (>= 2.0.0), |
| 29 |
- matrixStats, |
|
| 29 |
+ matrixStats (>= 0.50.0), |
|
| 30 | 30 |
permute |
| 31 | 31 |
Suggests: |
| 32 | 32 |
RUnit, |
From: Kasper Daniel Hansen <[email protected]>
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@114621 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 10/03/2016 17:06:33
From: Kasper Daniel Hansen <[email protected]>
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@114581 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 10/03/2016 02:44:17
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.7.2 |
|
| 2 |
+Version: 1.7.6 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| 5 | 5 |
sequencing data. |
| ... | ... |
@@ -26,7 +26,8 @@ Imports: |
| 26 | 26 |
data.table, |
| 27 | 27 |
S4Vectors, |
| 28 | 28 |
R.utils (>= 2.0.0), |
| 29 |
- matrixStats |
|
| 29 |
+ matrixStats, |
|
| 30 |
+ permute |
|
| 30 | 31 |
Suggests: |
| 31 | 32 |
RUnit, |
| 32 | 33 |
bsseqData, |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@111565 bc3139a8-67e5-0310-9ffc-ced21a209358
Herve Pages authored on 16/12/2015 21:21:51
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.7.1 |
|
| 2 |
+Version: 1.7.2 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| 5 | 5 |
sequencing data. |
| ... | ... |
@@ -10,12 +10,12 @@ Depends: |
| 10 | 10 |
R (>= 2.15), |
| 11 | 11 |
methods, |
| 12 | 12 |
BiocGenerics, |
| 13 |
- GenomicRanges (>= 1.19.6), |
|
| 13 |
+ GenomicRanges (>= 1.23.7), |
|
| 14 | 14 |
SummarizedExperiment (>= 0.1.1), |
| 15 | 15 |
parallel, |
| 16 | 16 |
limma |
| 17 | 17 |
Imports: |
| 18 |
- IRanges (>= 2.1.10), |
|
| 18 |
+ IRanges (>= 2.5.17), |
|
| 19 | 19 |
GenomeInfoDb, |
| 20 | 20 |
scales, |
| 21 | 21 |
stats, |
From: Kasper Daniel Hansen <[email protected]>
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@110074 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 29/10/2015 19:12:43
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.7.0 |
|
| 2 |
+Version: 1.7.1 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| 5 | 5 |
sequencing data. |
| ... | ... |
@@ -10,12 +10,13 @@ Depends: |
| 10 | 10 |
R (>= 2.15), |
| 11 | 11 |
methods, |
| 12 | 12 |
BiocGenerics, |
| 13 |
- IRanges (>= 2.1.10), |
|
| 14 | 13 |
GenomicRanges (>= 1.19.6), |
| 15 | 14 |
SummarizedExperiment (>= 0.1.1), |
| 16 | 15 |
parallel, |
| 17 |
- GenomeInfoDb |
|
| 16 |
+ limma |
|
| 18 | 17 |
Imports: |
| 18 |
+ IRanges (>= 2.1.10), |
|
| 19 |
+ GenomeInfoDb, |
|
| 19 | 20 |
scales, |
| 20 | 21 |
stats, |
| 21 | 22 |
graphics, |
| ... | ... |
@@ -29,7 +30,8 @@ Imports: |
| 29 | 30 |
Suggests: |
| 30 | 31 |
RUnit, |
| 31 | 32 |
bsseqData, |
| 32 |
- BiocStyle |
|
| 33 |
+ BiocStyle, |
|
| 34 |
+ knitr |
|
| 33 | 35 |
Collate: |
| 34 | 36 |
hasGRanges.R |
| 35 | 37 |
BSseq_class.R |
| ... | ... |
@@ -47,8 +49,12 @@ Collate: |
| 47 | 49 |
fisher.R |
| 48 | 50 |
permutations.R |
| 49 | 51 |
BSmooth.fstat.R |
| 52 |
+ BSseqStat_class.R |
|
| 53 |
+ getStats.R |
|
| 50 | 54 |
License: Artistic-2.0 |
| 55 |
+VignetteBuilder: knitr |
|
| 51 | 56 |
URL: https://github.com/kasperdanielhansen/bsseq |
| 52 |
-BugReports: https://github.com/kasperdanielhansen/bsseq/issues |
|
| 53 | 57 |
LazyData: yes |
| 58 |
+LazyDataCompression: xz |
|
| 59 |
+BugReports: https://github.com/kasperdanielhansen/bsseq/issues |
|
| 54 | 60 |
biocViews: DNAMethylation |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@109592 bc3139a8-67e5-0310-9ffc-ced21a209358
Dan Tenenbaum authored on 13/10/2015 19:59:53
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@109589 bc3139a8-67e5-0310-9ffc-ced21a209358
Dan Tenenbaum authored on 13/10/2015 19:36:05
From: Kasper Daniel Hansen <[email protected]>
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@106952 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 31/07/2015 15:56:54
Commit id: 21404fe8275c89f6f29231a680703827b0796ff9
Merge pull request #4 from PeteHaitch/master
Updates to read.bismark(), mostly documentation
Commit id: 6ba560784b0e6e6f2e8c40de72b4abf516dc14e3
Update tests and examples to use gzipped data. Ensure strand is kept for cytosineReport files if collapseStrand = FALSE.
Commit id: 41b003506ba63d0c7ec330c2ea0b826e0c1c5e9c
Remove Travis-CI. Not relevant at this juncture.
Commit id: 2fd84392d9f39409b6958f0ce0d77ea5e6476bee
Hardcode RVERSION in .travis.yml
Commit id: 127bc93e92cd065e94dbeac0001949e5c4138d91
Experimental Travis-CI support.
Commit id: a6fecb9692f9b72093d3e0e79cf39e325d63b1e9
Second pass at updating read.bismark() and docs. Updated DESCRIPTION in light of changes and added NEWS.rd entry.
Commit id: 5af9b047653567816174480a6f405e1d02f0a74b
First pass at re-write of read.bismark() and associated docs.
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@106909 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 30/07/2015 01:16:09
| ... | ... |
@@ -1,17 +1,52 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.5.4 |
|
| 2 |
+Version: 1.5.5 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 |
-Description: A collection of tools for analyzing and visualizing bisulfite sequencing data. |
|
| 4 |
+Description: A collection of tools for analyzing and visualizing bisulfite |
|
| 5 |
+ sequencing data. |
|
| 5 | 6 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
| 6 |
- email = "[email protected]")) |
|
| 7 |
-Depends: R (>= 2.15), methods, BiocGenerics, matrixStats, IRanges (>= 2.1.10), |
|
| 8 |
- GenomicRanges (>= 1.19.6), SummarizedExperiment (>= 0.1.1), parallel, |
|
| 9 |
- GenomeInfoDb |
|
| 10 |
-Imports: scales, stats, graphics, Biobase, locfit, gtools, data.table, S4Vectors |
|
| 11 |
-Suggests: RUnit, bsseqData, BiocStyle |
|
| 12 |
-Collate: hasGRanges.R BSseq_class.R BSseqTstat_class.R BSseq_utils.R combine.R |
|
| 13 |
- utils.R read.bsmooth.R read.bismark.R BSmooth.R BSmooth.tstat.R dmrFinder.R |
|
| 14 |
- gof_stats.R plotting.R fisher.R permutations.R |
|
| 7 |
+ email = "[email protected]"), |
|
| 8 |
+ person("Peter", "Hickey", role = "ctb", email = "[email protected]"))
|
|
| 9 |
+Depends: |
|
| 10 |
+ R (>= 2.15), |
|
| 11 |
+ methods, |
|
| 12 |
+ BiocGenerics, |
|
| 13 |
+ IRanges (>= 2.1.10), |
|
| 14 |
+ GenomicRanges (>= 1.19.6), |
|
| 15 |
+ SummarizedExperiment (>= 0.1.1), |
|
| 16 |
+ parallel, |
|
| 17 |
+ GenomeInfoDb |
|
| 18 |
+Imports: |
|
| 19 |
+ scales, |
|
| 20 |
+ stats, |
|
| 21 |
+ graphics, |
|
| 22 |
+ Biobase, |
|
| 23 |
+ locfit, |
|
| 24 |
+ gtools, |
|
| 25 |
+ data.table, |
|
| 26 |
+ S4Vectors, |
|
| 27 |
+ R.utils (>= 2.0.0), |
|
| 28 |
+ matrixStats |
|
| 29 |
+Suggests: |
|
| 30 |
+ RUnit, |
|
| 31 |
+ bsseqData, |
|
| 32 |
+ BiocStyle |
|
| 33 |
+Collate: |
|
| 34 |
+ hasGRanges.R |
|
| 35 |
+ BSseq_class.R |
|
| 36 |
+ BSseqTstat_class.R |
|
| 37 |
+ BSseq_utils.R |
|
| 38 |
+ combine.R |
|
| 39 |
+ utils.R |
|
| 40 |
+ read.bsmooth.R |
|
| 41 |
+ read.bismark.R |
|
| 42 |
+ BSmooth.R |
|
| 43 |
+ BSmooth.tstat.R |
|
| 44 |
+ dmrFinder.R |
|
| 45 |
+ gof_stats.R |
|
| 46 |
+ plotting.R |
|
| 47 |
+ fisher.R |
|
| 48 |
+ permutations.R |
|
| 49 |
+ BSmooth.fstat.R |
|
| 15 | 50 |
License: Artistic-2.0 |
| 16 | 51 |
URL: https://github.com/kasperdanielhansen/bsseq |
| 17 | 52 |
LazyData: yes |
Commit id: 8d2aa748f67c8ddf0ec55f642d46977856ade539
fixed conflicts
Commit id: 6f9f1acacef5e3f9639c13b0111f61f9c8cffd86
updated permutation code, DEPENDS order
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@105116 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 18/06/2015 13:47:20
| ... | ... |
@@ -4,9 +4,9 @@ Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: A collection of tools for analyzing and visualizing bisulfite sequencing data. |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
| 6 | 6 |
email = "[email protected]")) |
| 7 |
-Depends: R (>= 2.15), methods, BiocGenerics, IRanges (>= 2.1.10), |
|
| 8 |
- GenomicRanges (>= 1.19.6), SummarizedExperiment (>= 0.2.0), parallel, |
|
| 9 |
- matrixStats, GenomeInfoDb |
|
| 7 |
+Depends: R (>= 2.15), methods, BiocGenerics, matrixStats, IRanges (>= 2.1.10), |
|
| 8 |
+ GenomicRanges (>= 1.19.6), SummarizedExperiment (>= 0.1.1), parallel, |
|
| 9 |
+ GenomeInfoDb |
|
| 10 | 10 |
Imports: scales, stats, graphics, Biobase, locfit, gtools, data.table, S4Vectors |
| 11 | 11 |
Suggests: RUnit, bsseqData, BiocStyle |
| 12 | 12 |
Collate: hasGRanges.R BSseq_class.R BSseqTstat_class.R BSseq_utils.R combine.R |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@105069 bc3139a8-67e5-0310-9ffc-ced21a209358
Herve Pages authored on 17/06/2015 06:46:22
| ... | ... |
@@ -1,11 +1,11 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.5.3 |
|
| 2 |
+Version: 1.5.4 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: A collection of tools for analyzing and visualizing bisulfite sequencing data. |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
| 6 | 6 |
email = "[email protected]")) |
| 7 | 7 |
Depends: R (>= 2.15), methods, BiocGenerics, IRanges (>= 2.1.10), |
| 8 |
- GenomicRanges (>= 1.19.6), SummarizedExperiment (>= 0.1.1), parallel, |
|
| 8 |
+ GenomicRanges (>= 1.19.6), SummarizedExperiment (>= 0.2.0), parallel, |
|
| 9 | 9 |
matrixStats, GenomeInfoDb |
| 10 | 10 |
Imports: scales, stats, graphics, Biobase, locfit, gtools, data.table, S4Vectors |
| 11 | 11 |
Suggests: RUnit, bsseqData, BiocStyle |
Commit id: 3e3c4a483adc9ba1e5d101a35f9a0fef41d2b78b
updated vignettes to use BiocStyle
Commit id: fe749c1df8a2a39ca6c4e1cc3b2358195f307631
updating read.bismark
Commit id: c50eb68c8e7f1be51af4ff411c95064849b52d15
Fixing Description; updating bsseq.Rnw to use BiocStyle
Commit id: f38a77394f0248aae1a6a4e27102610a53ca892e
resaved with compress=xz
Commit id: 2dcedd4fead08fe0af2a0afb7de2c89f4818b962
added Raw parsing of cytosine report files from Bismark
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@104827 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 11/06/2015 14:04:52
| ... | ... |
@@ -1,14 +1,14 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.5.2 |
|
| 3 |
-Title: Analyze, manage and store bisulfite sequencing data. |
|
| 4 |
-Description: Tools for analyzing and visualizing bisulfite sequencing data |
|
| 2 |
+Version: 1.5.3 |
|
| 3 |
+Title: Analyze, manage and store bisulfite sequencing data |
|
| 4 |
+Description: A collection of tools for analyzing and visualizing bisulfite sequencing data. |
|
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
| 6 | 6 |
email = "[email protected]")) |
| 7 |
-Depends: R (>= 2.15), methods, BiocGenerics, S4Vectors, IRanges (>= 2.1.10), |
|
| 7 |
+Depends: R (>= 2.15), methods, BiocGenerics, IRanges (>= 2.1.10), |
|
| 8 | 8 |
GenomicRanges (>= 1.19.6), SummarizedExperiment (>= 0.1.1), parallel, |
| 9 | 9 |
matrixStats, GenomeInfoDb |
| 10 |
-Imports: scales, stats, graphics, Biobase, locfit, gtools |
|
| 11 |
-Suggests: RUnit, bsseqData |
|
| 10 |
+Imports: scales, stats, graphics, Biobase, locfit, gtools, data.table, S4Vectors |
|
| 11 |
+Suggests: RUnit, bsseqData, BiocStyle |
|
| 12 | 12 |
Collate: hasGRanges.R BSseq_class.R BSseqTstat_class.R BSseq_utils.R combine.R |
| 13 | 13 |
utils.R read.bsmooth.R read.bismark.R BSmooth.R BSmooth.tstat.R dmrFinder.R |
| 14 | 14 |
gof_stats.R plotting.R fisher.R permutations.R |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@103650 bc3139a8-67e5-0310-9ffc-ced21a209358
Herve Pages authored on 11/05/2015 21:38:11
| ... | ... |
@@ -1,11 +1,12 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.5.1 |
|
| 2 |
+Version: 1.5.2 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data. |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
| 6 | 6 |
email = "[email protected]")) |
| 7 | 7 |
Depends: R (>= 2.15), methods, BiocGenerics, S4Vectors, IRanges (>= 2.1.10), |
| 8 |
- GenomicRanges (>= 1.19.6), parallel, matrixStats, GenomeInfoDb |
|
| 8 |
+ GenomicRanges (>= 1.19.6), SummarizedExperiment (>= 0.1.1), parallel, |
|
| 9 |
+ matrixStats, GenomeInfoDb |
|
| 9 | 10 |
Imports: scales, stats, graphics, Biobase, locfit, gtools |
| 10 | 11 |
Suggests: RUnit, bsseqData |
| 11 | 12 |
Collate: hasGRanges.R BSseq_class.R BSseqTstat_class.R BSseq_utils.R combine.R |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@103443 bc3139a8-67e5-0310-9ffc-ced21a209358
Herve Pages authored on 04/05/2015 19:01:24
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.5.0 |
|
| 2 |
+Version: 1.5.1 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data. |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@102594 bc3139a8-67e5-0310-9ffc-ced21a209358
Dan Tenenbaum authored on 16/04/2015 20:02:44
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.4.0 |
|
| 2 |
+Version: 1.5.0 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data. |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@102591 bc3139a8-67e5-0310-9ffc-ced21a209358
Dan Tenenbaum authored on 16/04/2015 19:42:01
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.3.8 |
|
| 2 |
+Version: 1.4.0 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data. |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
Commit id: 6377cad91631a2ca863d78712c231090a296e36e
more permutations, more fixes for rowRanges
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@100803 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 18/03/2015 15:21:49
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.3.7 |
|
| 2 |
+Version: 1.3.8 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data. |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
Commit id: 2155bb403810b2744c1ee1c364aa2fe6216a6671
bumped version
Commit id: f2df86b5e594d94aa0fd591152f9121554dfc47c
more work on permutations; now including unitTests
Commit id: 040af54e133c6fad141f3047a5b5a60772642b33
unit test for permutation matrix
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@100731 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 16/03/2015 19:57:19
| ... | ... |
@@ -1,12 +1,12 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.3.6 |
|
| 2 |
+Version: 1.3.7 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data. |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
| 6 | 6 |
email = "[email protected]")) |
| 7 | 7 |
Depends: R (>= 2.15), methods, BiocGenerics, S4Vectors, IRanges (>= 2.1.10), |
| 8 | 8 |
GenomicRanges (>= 1.19.6), parallel, matrixStats, GenomeInfoDb |
| 9 |
-Imports: scales, stats, graphics, Biobase, locfit |
|
| 9 |
+Imports: scales, stats, graphics, Biobase, locfit, gtools |
|
| 10 | 10 |
Suggests: RUnit, bsseqData |
| 11 | 11 |
Collate: hasGRanges.R BSseq_class.R BSseqTstat_class.R BSseq_utils.R combine.R |
| 12 | 12 |
utils.R read.bsmooth.R read.bismark.R BSmooth.R BSmooth.tstat.R dmrFinder.R |
Commit id: 639d741f7b58e2fc156a5557606463447ccbf780
changed rowData to rowRanges
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@100717 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 16/03/2015 13:44:49
| ... | ... |
@@ -1,6 +1,6 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.3.5 |
|
| 3 |
-Title: Analyze, manage and store bisulfite sequencing data |
|
| 2 |
+Version: 1.3.6 |
|
| 3 |
+Title: Analyze, manage and store bisulfite sequencing data. |
|
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
| 6 | 6 |
email = "[email protected]")) |
Commit id: 39647ec7931bb858853926b053647d6d729ac067
added permutations.R to Collate
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@100644 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 13/03/2015 17:20:10
| ... | ... |
@@ -10,7 +10,7 @@ Imports: scales, stats, graphics, Biobase, locfit |
| 10 | 10 |
Suggests: RUnit, bsseqData |
| 11 | 11 |
Collate: hasGRanges.R BSseq_class.R BSseqTstat_class.R BSseq_utils.R combine.R |
| 12 | 12 |
utils.R read.bsmooth.R read.bismark.R BSmooth.R BSmooth.tstat.R dmrFinder.R |
| 13 |
- gof_stats.R plotting.R fisher.R |
|
| 13 |
+ gof_stats.R plotting.R fisher.R permutations.R |
|
| 14 | 14 |
License: Artistic-2.0 |
| 15 | 15 |
URL: https://github.com/kasperdanielhansen/bsseq |
| 16 | 16 |
LazyData: yes |
Commit id: cb084361bf813e05e2279000303be55e8d07107c
modified permutation code
Commit id: 083a52bc284f632f8c6e471d136bff88577b6813
permutation code, not exported
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@100482 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 10/03/2015 17:48:48
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.3.4 |
|
| 2 |
+Version: 1.3.5 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@97403 bc3139a8-67e5-0310-9ffc-ced21a209358
Herve Pages authored on 05/12/2014 06:14:38
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.3.3 |
|
| 2 |
+Version: 1.3.4 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
- on GenomicRanges::assayNames
- argument changed (from 'object' to 'x')
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@97133 bc3139a8-67e5-0310-9ffc-ced21a209358
Martin Morgan authored on 26/11/2014 02:32:58
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.3.2 |
|
| 2 |
+Version: 1.3.3 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@96631 bc3139a8-67e5-0310-9ffc-ced21a209358
Herve Pages authored on 08/11/2014 02:53:46
| ... | ... |
@@ -1,11 +1,11 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.3.1 |
|
| 2 |
+Version: 1.3.2 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
| 6 | 6 |
email = "[email protected]")) |
| 7 |
-Depends: R (>= 2.15), methods, BiocGenerics, IRanges, GenomicRanges, |
|
| 8 |
- parallel, matrixStats, GenomeInfoDb, S4Vectors |
|
| 7 |
+Depends: R (>= 2.15), methods, BiocGenerics, S4Vectors, IRanges (>= 2.1.10), |
|
| 8 |
+ GenomicRanges (>= 1.19.6), parallel, matrixStats, GenomeInfoDb |
|
| 9 | 9 |
Imports: scales, stats, graphics, Biobase, locfit |
| 10 | 10 |
Suggests: RUnit, bsseqData |
| 11 | 11 |
Collate: hasGRanges.R BSseq_class.R BSseqTstat_class.R BSseq_utils.R combine.R |
Commit information:
Commit id: 5ea7d2eb94ec7497dce8ddcfc971f324b38ded5f
bumped version
Committed by: Kasper Daniel Hansen
Author Name: Kasper Daniel Hansen
Commit date: 2014-10-28 11:42:23 -0400
Author date: 2014-10-28 11:42:23 -0400
Commit id: 137afbcd94987d9b7f6e9571282b1d6b927d8ea1
changed imports to support recent changes in the S4Vectors/GenomeInfoDb/GenomicRanges suite of packages
Committed by: Kasper Daniel Hansen
Author Name: Kasper Daniel Hansen
Commit date: 2014-10-28 11:41:56 -0400
Author date: 2014-10-28 11:41:56 -0400
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@96114 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 28/10/2014 15:42:30
| ... | ... |
@@ -1,11 +1,11 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.3.0 |
|
| 2 |
+Version: 1.3.1 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
| 6 | 6 |
email = "[email protected]")) |
| 7 | 7 |
Depends: R (>= 2.15), methods, BiocGenerics, IRanges, GenomicRanges, |
| 8 |
- parallel, matrixStats |
|
| 8 |
+ parallel, matrixStats, GenomeInfoDb, S4Vectors |
|
| 9 | 9 |
Imports: scales, stats, graphics, Biobase, locfit |
| 10 | 10 |
Suggests: RUnit, bsseqData |
| 11 | 11 |
Collate: hasGRanges.R BSseq_class.R BSseqTstat_class.R BSseq_utils.R combine.R |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@95443 bc3139a8-67e5-0310-9ffc-ced21a209358
Dan Tenenbaum authored on 13/10/2014 21:47:41
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.2.0 |
|
| 2 |
+Version: 1.3.0 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@95439 bc3139a8-67e5-0310-9ffc-ced21a209358
Dan Tenenbaum authored on 13/10/2014 21:38:33
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.1.2 |
|
| 2 |
+Version: 1.2.0 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
Commit information:
Commit id: 970b9726dd0d9bb72a11a3e4fc3308a9da3569ab
added GitHub url to DESCRIPTION
Committed by: Kasper Daniel Hansen
Author Name: Kasper Daniel Hansen
Commit date: 2014-09-21 13:05:37 -0400
Author date: 2014-09-21 13:05:37 -0400
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@94343 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 21/09/2014 17:05:44
| ... | ... |
@@ -12,5 +12,6 @@ Collate: hasGRanges.R BSseq_class.R BSseqTstat_class.R BSseq_utils.R combine.R |
| 12 | 12 |
utils.R read.bsmooth.R read.bismark.R BSmooth.R BSmooth.tstat.R dmrFinder.R |
| 13 | 13 |
gof_stats.R plotting.R fisher.R |
| 14 | 14 |
License: Artistic-2.0 |
| 15 |
+URL: https://github.com/kasperdanielhansen/bsseq |
|
| 15 | 16 |
LazyData: yes |
| 16 | 17 |
biocViews: DNAMethylation |
Commit information:
Commit id: 64613833bc6c16668d484639dc935ea5d721ec28
fixed various small issues like man pages, CITATION etc.
Committed by: Kasper Daniel Hansen
Author Name: Kasper Daniel Hansen
Commit date: 2014-09-21 12:44:59 -0400
Author date: 2014-09-21 12:44:59 -0400
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@94342 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 21/09/2014 16:45:10
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.1.1 |
|
| 2 |
+Version: 1.1.2 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
Commit information:
Commit id: dabf513da508265296e7715998fed372fd7662e2
Commit message:
updated maintainer email
Committed by Kasper Daniel Hansen <kasperdanielhansen at gmail.com>
Commit date: 2014-04-26T16:35:06-04:00
From: Bioconductor Git-SVN Bridge <[email protected]>
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@89534 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 26/04/2014 20:35:17
| ... | ... |
@@ -1,9 +1,9 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.1.0 |
|
| 2 |
+Version: 1.1.1 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
| 6 |
- email = "[email protected]")) |
|
| 6 |
+ email = "[email protected]")) |
|
| 7 | 7 |
Depends: R (>= 2.15), methods, BiocGenerics, IRanges, GenomicRanges, |
| 8 | 8 |
parallel, matrixStats |
| 9 | 9 |
Imports: scales, stats, graphics, Biobase, locfit |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@88840 bc3139a8-67e5-0310-9ffc-ced21a209358
Dan Tenenbaum authored on 11/04/2014 21:21:21
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.0.0 |
|
| 2 |
+Version: 1.1.0 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@88838 bc3139a8-67e5-0310-9ffc-ced21a209358
Dan Tenenbaum authored on 11/04/2014 21:07:21
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 0.99.0 |
|
| 2 |
+Version: 1.0.0 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
Commit information:
Commit id: 32762b6bb7445f8b4a96ff02b0edc20c1ef6a1e2
Commit message:
bumped version. Fixed unit test as per changes in SummarizedExperiment. Fixed use of :::
Committed by Kasper Daniel Hansen <kasperdanielhansen at gmail.com>
Commit date: 2014-03-22T22:57:39-04:00
Commit id: 9ddfece19dcb7771cab2136890646b4cb491725e
Commit message:
forgot to stage files in previous commit
Committed by Kasper Daniel Hansen <kasperdanielhansen at gmail.com>
Commit date: 2014-03-22T22:58:11-04:00
Commit id: 3b64624fffff66918dfbcb255ad38a34f63be09f
Commit message:
Merge branch 'master' of github.com:kasperdanielhansen/bsseq
Committed by Kasper Daniel Hansen <kasperdanielhansen at gmail.com>
Commit date: 2014-03-22T23:22:50-04:00
From: Bioconductor Git-SVN Bridge <[email protected]>
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@87756 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 23/03/2014 03:23:15
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 0.11.5 |
|
| 2 |
+Version: 0.99.0 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
| ... | ... |
@@ -10,7 +10,7 @@ Imports: scales, stats, graphics, Biobase, locfit |
| 10 | 10 |
Suggests: RUnit, bsseqData |
| 11 | 11 |
Collate: hasGRanges.R BSseq_class.R BSseqTstat_class.R BSseq_utils.R combine.R |
| 12 | 12 |
utils.R read.bsmooth.R read.bismark.R BSmooth.R BSmooth.tstat.R dmrFinder.R |
| 13 |
- gof_stats.R plotting.R fisher.R fixes.R |
|
| 13 |
+ gof_stats.R plotting.R fisher.R |
|
| 14 | 14 |
License: Artistic-2.0 |
| 15 | 15 |
LazyData: yes |
| 16 | 16 |
biocViews: DNAMethylation |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@86674 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 21/02/2014 14:46:59
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 0.11.4 |
|
| 2 |
+Version: 0.11.5 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@86580 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 19/02/2014 16:00:38
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 0.11.3 |
|
| 2 |
+Version: 0.11.4 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@86091 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 05/02/2014 03:40:31
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 0.11.2 |
|
| 2 |
+Version: 0.11.3 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@84769 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 17/12/2013 19:25:23
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 0.11.1 |
|
| 2 |
+Version: 0.11.2 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@83368 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 18/11/2013 04:25:21
| ... | ... |
@@ -1,9 +1,9 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 0.11.0 |
|
| 2 |
+Version: 0.11.1 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 |
-Author: Kasper Daniel Hansen |
|
| 6 |
-Maintainer: Kasper Daniel Hansen <[email protected]> |
|
| 5 |
+Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
|
|
| 6 |
+ email = "[email protected]")) |
|
| 7 | 7 |
Depends: R (>= 2.15), methods, BiocGenerics, IRanges, GenomicRanges, |
| 8 | 8 |
parallel, matrixStats |
| 9 | 9 |
Imports: scales, stats, graphics, Biobase, locfit |
| ... | ... |
@@ -14,4 +14,3 @@ Collate: hasGRanges.R BSseq_class.R BSseqTstat_class.R BSseq_utils.R combine.R |
| 14 | 14 |
License: Artistic-2.0 |
| 15 | 15 |
LazyData: yes |
| 16 | 16 |
biocViews: DNAMethylation |
| 17 |
-Packaged: 2012-07-10 04:15:29 UTC; khansen |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@81644 bc3139a8-67e5-0310-9ffc-ced21a209358
Dan Tenenbaum authored on 14/10/2013 21:47:19
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@81642 bc3139a8-67e5-0310-9ffc-ced21a209358
Dan Tenenbaum authored on 14/10/2013 21:29:21
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@81150 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 04/10/2013 15:23:24
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@80445 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 14/09/2013 15:06:17
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@78745 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 22/07/2013 16:21:43
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@78387 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 12/07/2013 20:53:31
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 0.9.7 |
|
| 2 |
+Version: 0.9.8 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Author: Kasper Daniel Hansen |
| ... | ... |
@@ -9,7 +9,7 @@ Depends: R (>= 2.15), methods, BiocGenerics, IRanges, GenomicRanges, |
| 9 | 9 |
Imports: scales, stats, graphics, Biobase, locfit |
| 10 | 10 |
Suggests: RUnit, bsseqData |
| 11 | 11 |
Collate: hasGRanges.R BSseq_class.R BSseqTstat_class.R BSseq_utils.R combine.R |
| 12 |
- utils.R read.bsmooth.R read.bismark.R BSmooth.R dmrFinder.R |
|
| 12 |
+ utils.R read.bsmooth.R read.bismark.R BSmooth.R BSmooth.tstat.R dmrFinder.R |
|
| 13 | 13 |
gof_stats.R plotting.R fisher.R fixes.R |
| 14 | 14 |
License: Artistic-2.0 |
| 15 | 15 |
LazyData: yes |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@78308 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 11/07/2013 01:40:33
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@78230 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 09/07/2013 20:12:29
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@78189 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 09/07/2013 01:30:03
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@78143 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 06/07/2013 21:26:40
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 0.9.3 |
|
| 2 |
+Version: 0.9.4 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Author: Kasper Daniel Hansen |
| ... | ... |
@@ -8,8 +8,9 @@ Depends: R (>= 2.15), methods, BiocGenerics, IRanges, GenomicRanges, |
| 8 | 8 |
parallel, matrixStats |
| 9 | 9 |
Imports: scales, stats, graphics, Biobase, locfit |
| 10 | 10 |
Suggests: RUnit, bsseqData |
| 11 |
-Collate: hasGRanges.R BSseq_class.R BSseq_utils.R utils.R read.bsmooth.R |
|
| 12 |
- read.bismark.R BSmooth.R dmrFinder.R gof_stats.R plotting.R fisher.R fixes.R |
|
| 11 |
+Collate: hasGRanges.R BSseq_class.R BSseqTstat_class.R BSseq_utils.R combine.R |
|
| 12 |
+ utils.R read.bsmooth.R read.bismark.R BSmooth.R dmrFinder.R |
|
| 13 |
+ gof_stats.R plotting.R fisher.R fixes.R |
|
| 13 | 14 |
License: Artistic-2.0 |
| 14 | 15 |
LazyData: yes |
| 15 | 16 |
biocViews: DNAMethylation |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@78085 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 03/07/2013 14:01:40
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@77938 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 26/06/2013 19:52:04
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@76822 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 23/05/2013 01:08:15
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@75270 bc3139a8-67e5-0310-9ffc-ced21a209358
Dan Tenenbaum authored on 03/04/2013 22:06:11
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@75263 bc3139a8-67e5-0310-9ffc-ced21a209358
Dan Tenenbaum authored on 03/04/2013 21:32:27
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@73977 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 06/03/2013 19:03:51
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@71547 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 29/11/2012 15:04:40
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@71341 bc3139a8-67e5-0310-9ffc-ced21a209358
Peter Hickey authored on 19/11/2012 22:53:38
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 0.7.2 |
|
| 2 |
+Version: 0.7.3 |
|
| 3 | 3 |
Title: Analyze, manage and store bisulfite sequencing data |
| 4 | 4 |
Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Author: Kasper Daniel Hansen |
| ... | ... |
@@ -8,8 +8,8 @@ Depends: R (>= 2.15), methods, BiocGenerics, IRanges, GenomicRanges, |
| 8 | 8 |
parallel, matrixStats |
| 9 | 9 |
Imports: scales, stats, graphics, Biobase, locfit |
| 10 | 10 |
Suggests: RUnit, bsseqData |
| 11 |
-Collate: hasGRanges.R BSseq_class.R BSseq_utils.R utils.R read.R |
|
| 12 |
- BSmooth.R dmrFinder.R gof_stats.R plotting.R fisher.R fixes.R |
|
| 11 |
+Collate: hasGRanges.R BSseq_class.R BSseq_utils.R utils.R read.bsmooth.R |
|
| 12 |
+ read.bismark.R BSmooth.R dmrFinder.R gof_stats.R plotting.R fisher.R fixes.R |
|
| 13 | 13 |
License: Artistic-2.0 |
| 14 | 14 |
LazyData: yes |
| 15 | 15 |
biocViews: DNAMethylation |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@70595 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 16/10/2012 19:35:29
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@70488 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 13/10/2012 16:48:16
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@70052 bc3139a8-67e5-0310-9ffc-ced21a209358
Dan Tenenbaum authored on 01/10/2012 22:43:56
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@70050 bc3139a8-67e5-0310-9ffc-ced21a209358
Dan Tenenbaum authored on 01/10/2012 22:16:24
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@68240 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 06/08/2012 03:03:11
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@68168 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 02/08/2012 20:56:42
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@67929 bc3139a8-67e5-0310-9ffc-ced21a209358
Marc Carlson authored on 20/07/2012 17:45:09
| 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,16 @@ |
| 1 |
+Package: bsseq |
|
| 2 |
+Version: 0.4.2 |
|
| 3 |
+Title: Analyze, manage and store bisulfite sequencing data |
|
| 4 |
+Description: Tools for analyzing and visualizing bisulfite sequencing data |
|
| 5 |
+Author: Kasper Daniel Hansen |
|
| 6 |
+Maintainer: Kasper Daniel Hansen <[email protected]> |
|
| 7 |
+Depends: R (>= 2.15), methods, BiocGenerics, IRanges, GenomicRanges, |
|
| 8 |
+ parallel, matrixStats |
|
| 9 |
+Imports: scales, stats, graphics, Biobase, locfit |
|
| 10 |
+Suggests: RUnit, bsseqData |
|
| 11 |
+Collate: hasGRanges.R BSseq_class.R BSseq_utils.R utils.R read.R |
|
| 12 |
+ BSmooth.R dmrFinder.R gof_stats.R plotting.R fisher.R fixes.R |
|
| 13 |
+License: Artistic-2.0 |
|
| 14 |
+LazyData: yes |
|
| 15 |
+biocViews: DNAMethylation |
|
| 16 |
+Packaged: 2012-07-10 04:15:29 UTC; khansen |