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  1. tidyCoverage
  2. DESCRIPTION
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_22 branch

A Wokaty authored on 29/10/2025 15:27:26
Showing 1 changed files
DESCRIPTION
History View file @ 283f96f
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: tidyCoverage
2 2 
 Title: Extract and aggregate genomic coverage over features of interest
3 
-Version: 1.6.0
3 
+Version: 1.7.0
4 4 
 Date: 2023-11-09
5 5 
 Authors@R:
6 6 
     person("Jacques", "Serizay", , "[email protected]",
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_22 branch

A Wokaty authored on 29/10/2025 15:27:26
Showing 1 changed files
DESCRIPTION
History View file @ 56ab248
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@@ -1,6 +1,6 @@
1 1 
 Package: tidyCoverage
2 2 
 Title: Extract and aggregate genomic coverage over features of interest
3 
-Version: 1.5.0
3 
+Version: 1.6.0
4 4 
 Date: 2023-11-09
5 5 
 Authors@R:
6 6 
     person("Jacques", "Serizay", , "[email protected]",
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_21 branch

A Wokaty authored on 15/04/2025 17:27:07
Showing 1 changed files
DESCRIPTION
History View file @ 7130a9e
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@@ -1,6 +1,6 @@
1 1 
 Package: tidyCoverage
2 2 
 Title: Extract and aggregate genomic coverage over features of interest
3 
-Version: 1.4.0
3 
+Version: 1.5.0
4 4 
 Date: 2023-11-09
5 5 
 Authors@R:
6 6 
     person("Jacques", "Serizay", , "[email protected]",
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_21 branch

A Wokaty authored on 15/04/2025 17:27:07
Showing 1 changed files
DESCRIPTION
History View file @ c8037ce
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@@ -1,6 +1,6 @@
1 1 
 Package: tidyCoverage
2 2 
 Title: Extract and aggregate genomic coverage over features of interest
3 
-Version: 1.3.0
3 
+Version: 1.4.0
4 4 
 Date: 2023-11-09
5 5 
 Authors@R:
6 6 
     person("Jacques", "Serizay", , "[email protected]",
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_20 branch

J Wokaty authored on 29/10/2024 15:26:50
Showing 1 changed files
DESCRIPTION
History View file @ defcab5
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: tidyCoverage
2 2 
 Title: Extract and aggregate genomic coverage over features of interest
3 
-Version: 1.2.0
3 
+Version: 1.3.0
4 4 
 Date: 2023-11-09
5 5 
 Authors@R:
6 6 
     person("Jacques", "Serizay", , "[email protected]",
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_20 branch

J Wokaty authored on 29/10/2024 15:26:50
Showing 1 changed files
DESCRIPTION
History View file @ cd53efe
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: tidyCoverage
2 2 
 Title: Extract and aggregate genomic coverage over features of interest
3 
-Version: 1.1.2
3 
+Version: 1.2.0
4 4 
 Date: 2023-11-09
5 5 
 Authors@R:
6 6 
     person("Jacques", "Serizay", , "[email protected]",
Browse code

bump to v1.1.2

js2264 authored on 28/08/2024 20:55:48
Showing 1 changed files
DESCRIPTION
History View file @ d2f5e79
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: tidyCoverage
2 2 
 Title: Extract and aggregate genomic coverage over features of interest
3 
-Version: 1.1.1
3 
+Version: 1.1.2
4 4 
 Date: 2023-11-09
5 5 
 Authors@R:
6 6 
     person("Jacques", "Serizay", , "[email protected]",
Browse code

bump to v1.1.1

js2264 authored on 25/07/2024 21:37:05
Showing 1 changed files
DESCRIPTION
History View file @ cc28588
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: tidyCoverage
2 2 
 Title: Extract and aggregate genomic coverage over features of interest
3 
-Version: 1.1.0
3 
+Version: 1.1.1
4 4 
 Date: 2023-11-09
5 5 
 Authors@R:
6 6 
     person("Jacques", "Serizay", , "[email protected]",
... ... 
@@ -54,7 +54,6 @@ Suggests:
54 54 
     BiocStyle,
55 55 
     hues,
56 56 
     knitr,
57 
-    quarto,
58 57 
     rmarkdown,
59 58 
     sessioninfo,
60 59 
     testthat (>= 3.0.0)
Browse code

Merge remote-tracking branch 'upstream/devel' into devel

js2264 authored on 25/07/2024 15:47:50
Showing 0 changed files
Browse code

feat: more geoms

Jacques authored on 12/07/2024 20:56:30
Showing 1 changed files
DESCRIPTION
History View file @ f85d4dc
... ... 
@@ -40,6 +40,7 @@ Imports:
40 40 
     fansi,
41 41 
     pillar,
42 42 
     rlang,
43 
+    scales,
43 44 
     cli,
44 45 
     purrr,
45 46 
     vctrs,
Browse code

fix: add new quarto dep

js2264 authored on 12/07/2024 12:10:55
Showing 1 changed files
DESCRIPTION
History View file @ ab2090a
... ... 
@@ -53,6 +53,7 @@ Suggests:
53 53 
     BiocStyle,
54 54 
     hues,
55 55 
     knitr,
56 
+    quarto,
56 57 
     rmarkdown,
57 58 
     sessioninfo,
58 59 
     testthat (>= 3.0.0)
Browse code

feat: geom_aggrcoverage

js2264 authored on 11/07/2024 19:47:26
Showing 1 changed files
DESCRIPTION
History View file @ d0c89d4
... ... 
@@ -35,6 +35,7 @@ Imports:
35 35 
     rtracklayer,
36 36 
     methods,
37 37 
     tidyr,
38 
+    ggplot2,
38 39 
     dplyr,
39 40 
     fansi,
40 41 
     pillar,
... ... 
@@ -46,7 +47,6 @@ Imports:
46 47 
 Suggests:
47 48 
     tidySummarizedExperiment,
48 49 
     plyranges,
49 
-    ggplot2,
50 50 
     TxDb.Hsapiens.UCSC.hg19.knownGene,
51 51 
     AnnotationHub,
52 52 
     GenomicFeatures,
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_19 branch

J Wokaty authored on 30/04/2024 15:53:44
Showing 1 changed files
DESCRIPTION
History View file @ 4ff03fe
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: tidyCoverage
2 2 
 Title: Extract and aggregate genomic coverage over features of interest
3 
-Version: 1.0.0
3 
+Version: 1.1.0
4 4 
 Date: 2023-11-09
5 5 
 Authors@R:
6 6 
     person("Jacques", "Serizay", , "[email protected]",
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_19 branch

J Wokaty authored on 30/04/2024 15:53:44
Showing 1 changed files
DESCRIPTION
History View file @ c67a165
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: tidyCoverage
2 2 
 Title: Extract and aggregate genomic coverage over features of interest
3 
-Version: 0.99.5
3 
+Version: 1.0.0
4 4 
 Date: 2023-11-09
5 5 
 Authors@R:
6 6 
     person("Jacques", "Serizay", , "[email protected]",
Browse code

bump to v0.99.5

js2264 authored on 31/03/2024 12:09:18
Showing 1 changed files
DESCRIPTION
History View file @ 8a577d5
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: tidyCoverage
2 2 
 Title: Extract and aggregate genomic coverage over features of interest
3 
-Version: 0.99.4
3 
+Version: 0.99.5
4 4 
 Date: 2023-11-09
5 5 
 Authors@R:
6 6 
     person("Jacques", "Serizay", , "[email protected]",
Browse code

bump to v0.99.4

js2264 authored on 09/01/2024 12:06:54
Showing 1 changed files
DESCRIPTION
History View file @ 17d83fc
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: tidyCoverage
2 2 
 Title: Extract and aggregate genomic coverage over features of interest
3 
-Version: 0.99.3
3 
+Version: 0.99.4
4 4 
 Date: 2023-11-09
5 5 
 Authors@R:
6 6 
     person("Jacques", "Serizay", , "[email protected]",
... ... 
@@ -17,7 +17,8 @@ URL: https://github.com/js2264/tidyCoverage
17 17 
 BugReports: https://github.com/js2264/tidyCoverage/issues
18 18 
 biocViews:
19 19 
     Software,
20 
-    Coverage
20 
+    Sequencing,
21 
+    Coverage,
21 22 
 Encoding: UTF-8
22 23 
 Roxygen: list(markdown = TRUE)
23 24 
 RoxygenNote: 7.2.3
Browse code

bump to v0.99.3

js2264 authored on 09/01/2024 11:04:12
Showing 1 changed files
DESCRIPTION
History View file @ 68332f1
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: tidyCoverage
2 2 
 Title: Extract and aggregate genomic coverage over features of interest
3 
-Version: 0.99.2
3 
+Version: 0.99.3
4 4 
 Date: 2023-11-09
5 5 
 Authors@R:
6 6 
     person("Jacques", "Serizay", , "[email protected]",
... ... 
@@ -9,7 +9,7 @@ Description: `tidyCoverage` framework enables tidy manipulation
9 9 
     of collections of genomic tracks and features using
10 10 
     `tidySummarizedExperiment` methods. It facilitates the
11 11 
     extraction, aggregation and visualization of genomic coverage over
12 
-    individual of thousands of genomic loci, relying on `CoverageExperiment`
12 
+    individual or thousands of genomic loci, relying on `CoverageExperiment`
13 13 
     and `AggregatedCoverage` classes. This accelerates the integration
14 14 
     of genomic track data in genomic analysis workflows.
15 15 
 License: MIT + file LICENSE
Browse code

bump to v0.99.2

js2264 authored on 11/12/2023 22:39:20
Showing 1 changed files
DESCRIPTION
History View file @ 35af476
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: tidyCoverage
2 2 
 Title: Extract and aggregate genomic coverage over features of interest
3 
-Version: 0.99.1
3 
+Version: 0.99.2
4 4 
 Date: 2023-11-09
5 5 
 Authors@R:
6 6 
     person("Jacques", "Serizay", , "[email protected]",
Browse code

bump to v0.99.1

js2264 authored on 11/12/2023 22:33:56
Showing 1 changed files
DESCRIPTION
History View file @ e4d10b0
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: tidyCoverage
2 2 
 Title: Extract and aggregate genomic coverage over features of interest
3 
-Version: 0.99.0
3 
+Version: 0.99.1
4 4 
 Date: 2023-11-09
5 5 
 Authors@R:
6 6 
     person("Jacques", "Serizay", , "[email protected]",
Browse code

fix: NAMESPACE

js2264 authored on 11/12/2023 22:07:55
Showing 1 changed files
DESCRIPTION
History View file @ 7fcd589
... ... 
@@ -30,6 +30,7 @@ Imports:
30 30 
     GenomicRanges,
31 31 
     GenomeInfoDb,
32 32 
     BiocParallel,
33 
+    BiocIO,
33 34 
     rtracklayer,
34 35 
     methods,
35 36 
     tidyr,
Browse code

bump to 0.99.0

js2264 authored on 05/12/2023 20:20:00
Showing 1 changed files
DESCRIPTION
History View file @ 6df95c1
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: tidyCoverage
2 2 
 Title: Extract and aggregate genomic coverage over features of interest
3 
-Version: 0.98.1
3 
+Version: 0.99.0
4 4 
 Date: 2023-11-09
5 5 
 Authors@R:
6 6 
     person("Jacques", "Serizay", , "[email protected]",
Browse code

bump to 0.98.1

js2264 authored on 05/12/2023 09:00:03
Showing 1 changed files
DESCRIPTION
History View file @ c37a69b
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: tidyCoverage
2 2 
 Title: Extract and aggregate genomic coverage over features of interest
3 
-Version: 0.98.0
3 
+Version: 0.98.1
4 4 
 Date: 2023-11-09
5 5 
 Authors@R:
6 6 
     person("Jacques", "Serizay", , "[email protected]",
Browse code

doc: improve vignette

js2264 authored on 28/11/2023 07:06:57
Showing 1 changed files
DESCRIPTION
History View file @ 96337ba
... ... 
@@ -49,6 +49,7 @@ Suggests:
49 49 
     AnnotationHub,
50 50 
     GenomicFeatures,
51 51 
     BiocStyle,
52 
+    hues,
52 53 
     knitr,
53 54 
     rmarkdown,
54 55 
     sessioninfo,
Browse code

rename package to tidyCoverage

js2264 authored on 27/11/2023 11:55:03
Showing 1 changed files
DESCRIPTION
History View file @ b40402d
... ... 
@@ -1,14 +1,20 @@
1 
-Package: CoverageExperiment
2 
-Title: Aggregate coverage over aligned genomic features of interest
1 
+Package: tidyCoverage
2 
+Title: Extract and aggregate genomic coverage over features of interest
3 3 
 Version: 0.98.0
4 4 
 Date: 2023-11-09
5 5 
 Authors@R:
6 6 
     person("Jacques", "Serizay", , "[email protected]",
7 7 
         role = c("aut", "cre"))
8 
-Description: What the package does (one paragraph).
8 
+Description: `tidyCoverage` framework enables tidy manipulation
9 
+    of collections of genomic tracks and features using
10 
+    `tidySummarizedExperiment` methods. It facilitates the
11 
+    extraction, aggregation and visualization of genomic coverage over
12 
+    individual of thousands of genomic loci, relying on `CoverageExperiment`
13 
+    and `AggregatedCoverage` classes. This accelerates the integration
14 
+    of genomic track data in genomic analysis workflows.
9 15 
 License: MIT + file LICENSE
10 
-URL: https://github.com/js2264/CoverageExperiment
11 
-BugReports: https://github.com/js2264/CoverageExperiment/issues
16 
+URL: https://github.com/js2264/tidyCoverage
17 
+BugReports: https://github.com/js2264/tidyCoverage/issues
12 18 
 biocViews:
13 19 
     Software,
14 20 
     Coverage
Browse code

doc: update

js2264 authored on 27/11/2023 11:38:54
Showing 1 changed files
DESCRIPTION
History View file @ 031b5af
... ... 
@@ -26,6 +26,7 @@ Imports:
26 26 
     BiocParallel,
27 27 
     rtracklayer,
28 28 
     methods,
29 
+    tidyr,
29 30 
     dplyr,
30 31 
     fansi,
31 32 
     pillar,
... ... 
@@ -33,7 +34,6 @@ Imports:
33 34 
     cli,
34 35 
     purrr,
35 36 
     vctrs,
36 
-    vctrs
37 37 
     stats
38 38 
 Suggests:
39 39 
     tidySummarizedExperiment,
Browse code

feat: as_tibble for CoverageExperiment as well

js2264 authored on 27/11/2023 10:40:16
Showing 1 changed files
DESCRIPTION
History View file @ 2ba8a4f
... ... 
@@ -9,12 +9,14 @@ Description: What the package does (one paragraph).
9 9 
 License: MIT + file LICENSE
10 10 
 URL: https://github.com/js2264/CoverageExperiment
11 11 
 BugReports: https://github.com/js2264/CoverageExperiment/issues
12 
-biocViews: Software
12 
+biocViews:
13 
+    Software,
14 
+    Coverage
13 15 
 Encoding: UTF-8
14 16 
 Roxygen: list(markdown = TRUE)
15 17 
 RoxygenNote: 7.2.3
16 18 
 Depends:
17 
-    R (>= 2.10),
19 
+    R (>= 4.3.0),
18 20 
     SummarizedExperiment
19 21 
 Imports:
20 22 
     S4Vectors,
... ... 
@@ -30,7 +32,9 @@ Imports:
30 32 
     rlang,
31 33 
     cli,
32 34 
     purrr,
35 
+    vctrs,
33 36 
     vctrs
37 
+    stats
34 38 
 Suggests:
35 39 
     tidySummarizedExperiment,
36 40 
     plyranges,
Browse code

feat: can flip coverage according to strandness

js2264 authored on 26/11/2023 00:21:53
Showing 1 changed files
DESCRIPTION
History View file @ 957d8fb
... ... 
@@ -22,6 +22,7 @@ Imports:
22 22 
     GenomicRanges,
23 23 
     GenomeInfoDb,
24 24 
     BiocParallel,
25 
+    rtracklayer,
25 26 
     methods,
26 27 
     dplyr,
27 28 
     fansi,
... ... 
@@ -33,7 +34,6 @@ Imports:
33 34 
 Suggests:
34 35 
     tidySummarizedExperiment,
35 36 
     plyranges,
36 
-    rtracklayer,
37 37 
     ggplot2,
38 38 
     TxDb.Hsapiens.UCSC.hg19.knownGene,
39 39 
     AnnotationHub,
Browse code

feat: define CoverageExperiment and AggregatedCoverage classes and aggregate methods

js2264 authored on 25/11/2023 23:50:46
Showing 1 changed files
DESCRIPTION
History View file @ 1951d87
... ... 
@@ -1,14 +1,14 @@
1 1 
 Package: CoverageExperiment
2 
-Title: Coverage metrics over aligned genomic features of interest
2 
+Title: Aggregate coverage over aligned genomic features of interest
3 3 
 Version: 0.98.0
4 4 
 Date: 2023-11-09
5 5 
 Authors@R:
6 
-    person("First", "Last", , "[email protected]", role = c("aut", "cre"),
7 
-           comment = c(ORCID = "YOUR-ORCID-ID"))
6 
+    person("Jacques", "Serizay", , "[email protected]",
7 
+        role = c("aut", "cre"))
8 8 
 Description: What the package does (one paragraph).
9 9 
 License: MIT + file LICENSE
10 
-URL:
11 
-BugReports: https://support.bioconductor.org/tag/CoverageExperiment
10 
+URL: https://github.com/js2264/CoverageExperiment
11 
+BugReports: https://github.com/js2264/CoverageExperiment/issues
12 12 
 biocViews: Software
13 13 
 Encoding: UTF-8
14 14 
 Roxygen: list(markdown = TRUE)
... ... 
@@ -46,14 +46,3 @@ Suggests:
46 46 
 Config/testthat/edition: 3
47 47 
 VignetteBuilder: knitr
48 48 
 LazyData: false
49 
-Collate:
50 
-    'AllClasses.R'
51 
-    'AllGenerics.R'
52 
-    'AllMethods.R'
53 
-    'CoverageExperiment.R'
54 
-    'aggregate.R'
55 
-    'data.R'
56 
-    'globals.R'
57 
-    'print.R'
58 
-    'reexports.R'
59 
-    'utils.R'
Browse code

first push

js2264 authored on 25/11/2023 08:25:58
Showing 1 changed files
DESCRIPTION
History View file @ 4a79c07
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,59 @@
1 
+Package: CoverageExperiment
2 
+Title: Coverage metrics over aligned genomic features of interest
3 
+Version: 0.98.0
4 
+Date: 2023-11-09
5 
+Authors@R:
6 
+    person("First", "Last", , "[email protected]", role = c("aut", "cre"),
7 
+           comment = c(ORCID = "YOUR-ORCID-ID"))
8 
+Description: What the package does (one paragraph).
9 
+License: MIT + file LICENSE
10 
+URL:
11 
+BugReports: https://support.bioconductor.org/tag/CoverageExperiment
12 
+biocViews: Software
13 
+Encoding: UTF-8
14 
+Roxygen: list(markdown = TRUE)
15 
+RoxygenNote: 7.2.3
16 
+Depends:
17 
+    R (>= 2.10),
18 
+    SummarizedExperiment
19 
+Imports:
20 
+    S4Vectors,
21 
+    IRanges,
22 
+    GenomicRanges,
23 
+    GenomeInfoDb,
24 
+    BiocParallel,
25 
+    methods,
26 
+    dplyr,
27 
+    fansi,
28 
+    pillar,
29 
+    rlang,
30 
+    cli,
31 
+    purrr,
32 
+    vctrs
33 
+Suggests:
34 
+    tidySummarizedExperiment,
35 
+    plyranges,
36 
+    rtracklayer,
37 
+    ggplot2,
38 
+    TxDb.Hsapiens.UCSC.hg19.knownGene,
39 
+    AnnotationHub,
40 
+    GenomicFeatures,
41 
+    BiocStyle,
42 
+    knitr,
43 
+    rmarkdown,
44 
+    sessioninfo,
45 
+    testthat (>= 3.0.0)
46 
+Config/testthat/edition: 3
47 
+VignetteBuilder: knitr
48 
+LazyData: false
49 
+Collate:
50 
+    'AllClasses.R'
51 
+    'AllGenerics.R'
52 
+    'AllMethods.R'
53 
+    'CoverageExperiment.R'
54 
+    'aggregate.R'
55 
+    'data.R'
56 
+    'globals.R'
57 
+    'print.R'
58 
+    'reexports.R'
59 
+    'utils.R'