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  1. XeniumIO
  2. DESCRIPTION
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bump x.y.z version to odd y following creation of RELEASE_3_22 branch

A Wokaty authored on 29/10/2025 15:34:29
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 1.2.0
4 
+Version: 1.3.0
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
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 15:34:29
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 1.1.3
4 
+Version: 1.2.0
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
Browse code

version bump 1.1.3

LiNk-NY authored on 03/07/2025 20:58:11
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 1.1.2
4 
+Version: 1.1.3
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
Browse code

version bump 1.1.2

LiNk-NY authored on 06/05/2025 22:23:23
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 1.1.1
4 
+Version: 1.1.2
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
Browse code

version bump 1.1.1

LiNk-NY authored on 28/04/2025 18:21:07
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DESCRIPTION
History View file @ 1bc6759
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@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 1.1.0
4 
+Version: 1.1.1
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
Browse code

update R version dep due to pipe

LiNk-NY authored on 28/04/2025 18:21:05
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DESCRIPTION
History View file @ 403ae74
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@@ -14,7 +14,7 @@ Description: The package allows users to readily import spatial data
14 14 
     'parquet', 'h5', and 'mtx' files. The package mainly represents data
15 15 
     as SpatialExperiment objects.
16 16 
 License: Artistic-2.0
17 
-Depends: TENxIO
17 
+Depends: TENxIO, R (>= 4.5.0)
18 18 
 Imports:
19 19 
     BiocBaseUtils,
20 20 
     BiocGenerics,
Browse code

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

A Wokaty authored on 15/04/2025 17:47:31
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 1.0.0
4 
+Version: 1.1.0
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
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 17:47:31
Showing 1 changed files
DESCRIPTION
History View file @ b7166d4
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@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 0.99.9
4 
+Version: 1.0.0
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
Browse code

version bump 0.99.9

LiNk-NY authored on 04/04/2025 19:22:26
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DESCRIPTION
History View file @ eb592ac
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@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 0.99.8
4 
+Version: 0.99.9
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
... ... 
@@ -45,4 +45,4 @@ Collate:
45 45 
     'TENxXenium-class.R'
46 46 
     'XeniumIO-package.R'
47 47 
     'utilities.R'
48 
-Date: 2025-02-11
48 
+Date: 2025-04-04
Browse code

version bump 0.99.8

LiNk-NY authored on 11/02/2025 17:30:14
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DESCRIPTION
History View file @ 5e97a63
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@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 0.99.7
4 
+Version: 0.99.8
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
Browse code

version bump 0.99.7

LiNk-NY authored on 11/02/2025 17:12:25
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DESCRIPTION
History View file @ 7799b22
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@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 0.99.6
4 
+Version: 0.99.7
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
... ... 
@@ -45,4 +45,4 @@ Collate:
45 45 
     'TENxXenium-class.R'
46 46 
     'XeniumIO-package.R'
47 47 
     'utilities.R'
48 
-Date: 2025-02-10
48 
+Date: 2025-02-11
Browse code

version bump 0.99.6

LiNk-NY authored on 10/02/2025 22:48:18
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DESCRIPTION
History View file @ eb3528d
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@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 0.99.5
4 
+Version: 0.99.6
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
... ... 
@@ -45,4 +45,4 @@ Collate:
45 45 
     'TENxXenium-class.R'
46 46 
     'XeniumIO-package.R'
47 47 
     'utilities.R'
48 
-Date: 2024-12-06
48 
+Date: 2025-02-10
Browse code

version bump 0.99.5

LiNk-NY authored on 06/12/2024 16:42:25
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DESCRIPTION
History View file @ 9bcc803
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@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 0.99.4
4 
+Version: 0.99.5
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
... ... 
@@ -45,4 +45,4 @@ Collate:
45 45 
     'TENxXenium-class.R'
46 46 
     'XeniumIO-package.R'
47 47 
     'utilities.R'
48 
-Date: 2024-12-05
48 
+Date: 2024-12-06
Browse code

version bump 0.99.4

LiNk-NY authored on 05/12/2024 22:44:21
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DESCRIPTION
History View file @ 0fe98eb
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@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 0.99.3
4 
+Version: 0.99.4
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
Browse code

version bump 0.99.3

LiNk-NY authored on 05/12/2024 22:28:32
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DESCRIPTION
History View file @ e6ac63b
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@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 0.99.2
4 
+Version: 0.99.3
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
Browse code

version bump 0.99.2

LiNk-NY authored on 05/12/2024 21:51:23
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DESCRIPTION
History View file @ c79f3b7
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@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 0.99.1
4 
+Version: 0.99.2
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
Browse code

version bump 0.99.1

LiNk-NY authored on 05/12/2024 21:00:19
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DESCRIPTION
History View file @ 58b2321
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@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 0.99.0
4 
+Version: 0.99.1
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
... ... 
@@ -45,4 +45,4 @@ Collate:
45 45 
     'TENxXenium-class.R'
46 46 
     'XeniumIO-package.R'
47 47 
     'utilities.R'
48 
-Date: 2024-10-23
48 
+Date: 2024-12-05
Browse code

download and cache tiny_outs zip file & run examples / vignette

LiNk-NY authored on 05/12/2024 19:43:36
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DESCRIPTION
History View file @ 7d0e028
... ... 
@@ -28,6 +28,7 @@ Imports:
28 28 
     VisiumIO
29 29 
 Suggests:
30 30 
     arrow,
31 
+    BiocFileCache,
31 32 
     BiocStyle,
32 33 
     knitr,
33 34 
     rmarkdown,
Browse code

fix Description typo

LiNk-NY authored on 05/12/2024 19:42:11
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DESCRIPTION
History View file @ e6a801b
... ... 
@@ -10,7 +10,7 @@ Authors@R: c(
10 10 
     person("Estella", "Dong", role = "ctb")
11 11 
     )
12 12 
 Description: The package allows users to readily import spatial data
13 
-    obtain from the 10X Xenium Analyzer pipeline. Supported formats include
13 
+    obtained from the 10X Xenium Analyzer pipeline. Supported formats include
14 14 
     'parquet', 'h5', and 'mtx' files. The package mainly represents data
15 15 
     as SpatialExperiment objects.
16 16 
 License: Artistic-2.0
Browse code

update version number

LiNk-NY authored on 24/10/2024 14:57:47
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DESCRIPTION
History View file @ 7821e44
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@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 0.0.9
4 
+Version: 0.99.0
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
Browse code

version bump 0.0.9

LiNk-NY authored on 23/10/2024 20:40:49
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DESCRIPTION
History View file @ 4326776
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@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 0.0.8
4 
+Version: 0.0.9
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
... ... 
@@ -44,4 +44,4 @@ Collate:
44 44 
     'TENxXenium-class.R'
45 45 
     'XeniumIO-package.R'
46 46 
     'utilities.R'
47 
-Date: 2024-10-17
47 
+Date: 2024-10-23
Browse code

version bump 0.0.8

LiNk-NY authored on 17/10/2024 18:38:04
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DESCRIPTION
History View file @ ee86c74
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@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 0.0.7
4 
+Version: 0.0.8
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
... ... 
@@ -44,4 +44,4 @@ Collate:
44 44 
     'TENxXenium-class.R'
45 45 
     'XeniumIO-package.R'
46 46 
     'utilities.R'
47 
-Date: 2024-10-16
47 
+Date: 2024-10-17
Browse code

version bump 0.0.7

LiNk-NY authored on 16/10/2024 20:33:40
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DESCRIPTION
History View file @ 5912f31
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 0.0.6
4 
+Version: 0.0.7
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
... ... 
@@ -44,4 +44,4 @@ Collate:
44 44 
     'TENxXenium-class.R'
45 45 
     'XeniumIO-package.R'
46 46 
     'utilities.R'
47 
-Date: 2024-10-04
47 
+Date: 2024-10-16
Browse code

version bump 0.0.6

LiNk-NY authored on 16/10/2024 20:11:20
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DESCRIPTION
History View file @ 380bebe
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 0.0.5
4 
+Version: 0.0.6
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
Browse code

version bump 0.0.5

LiNk-NY authored on 04/10/2024 19:45:14
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DESCRIPTION
History View file @ bf945c8
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@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 0.0.4
4 
+Version: 0.0.5
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
... ... 
@@ -44,4 +44,4 @@ Collate:
44 44 
     'TENxXenium-class.R'
45 45 
     'XeniumIO-package.R'
46 46 
     'utilities.R'
47 
-Date: 2024-10-03
47 
+Date: 2024-10-04
Browse code

version bump 0.0.4

LiNk-NY authored on 03/10/2024 22:18:30
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DESCRIPTION
History View file @ 3cde629
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@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 0.0.3
4 
+Version: 0.0.4
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
Browse code

version bump 0.0.3

LiNk-NY authored on 03/10/2024 22:03:06
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DESCRIPTION
History View file @ 6e78b15
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@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 0.0.2
4 
+Version: 0.0.3
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
Browse code

version bump 0.0.2

LiNk-NY authored on 03/10/2024 21:26:24
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DESCRIPTION
History View file @ 7a18e79
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 0.0.1
4 
+Version: 0.0.2
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
... ... 
@@ -44,3 +44,4 @@ Collate:
44 44 
     'TENxXenium-class.R'
45 45 
     'XeniumIO-package.R'
46 46 
     'utilities.R'
47 
+Date: 2024-10-03
Browse code

bump version 0.0.1

LiNk-NY authored on 03/10/2024 21:16:57
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DESCRIPTION
History View file @ 8b93699
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: XeniumIO
2 2 
 Type: Package
3 3 
 Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
-Version: 0.0.0001
4 
+Version: 0.0.1
5 5 
 Authors@R: c(
6 6 
     person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 7 
         c(ORCID = "0000-0002-3242-0582")
Browse code

update import TENxXenium method, XeniumFile class docs

LiNk-NY authored on 03/10/2024 21:16:23
Showing 1 changed files
DESCRIPTION
History View file @ f5800b1
... ... 
@@ -17,9 +17,14 @@ License: Artistic-2.0
17 17 
 Depends: TENxIO
18 18 
 Imports:
19 19 
     BiocBaseUtils,
20 
+    BiocGenerics,
21 
+    BiocIO,
22 
+    jsonlite,
20 23 
     methods,
21 24 
     S4Vectors,
25 
+    SingleCellExperiment,
22 26 
     SpatialExperiment,
27 
+    SummarizedExperiment,
23 28 
     VisiumIO
24 29 
 Suggests:
25 30 
     arrow,
Browse code

add XeniumFile class for metadata

LiNk-NY authored on 03/10/2024 19:35:17
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DESCRIPTION
History View file @ 317e868
... ... 
@@ -34,3 +34,8 @@ Roxygen: list(markdown = TRUE)
34 34 
 RoxygenNote: 7.3.2
35 35 
 BugReports: https://github.com/waldronlab/XeniumIO/issues
36 36 
 URL: https://github.com/waldronlab/XeniumIO
37 
+Collate:
38 
+    'XeniumFile.R'
39 
+    'TENxXenium-class.R'
40 
+    'XeniumIO-package.R'
41 
+    'utilities.R'
Browse code

initial commit

LiNk-NY authored on 01/10/2024 21:09:50
Showing 1 changed files
DESCRIPTION
History View file @ c181621
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,36 @@
1 
+Package: XeniumIO
2 
+Type: Package
3 
+Title: Import and represent Xenium data from the 10X Xenium Analyzer
4 
+Version: 0.0.0001
5 
+Authors@R: c(
6 
+    person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
7 
+        c(ORCID = "0000-0002-3242-0582")
8 
+    ),
9 
+    person("Dario", "Righelli", role = "ctb"),
10 
+    person("Estella", "Dong", role = "ctb")
11 
+    )
12 
+Description: The package allows users to readily import spatial data
13 
+    obtain from the 10X Xenium Analyzer pipeline. Supported formats include
14 
+    'parquet', 'h5', and 'mtx' files. The package mainly represents data
15 
+    as SpatialExperiment objects.
16 
+License: Artistic-2.0
17 
+Depends: TENxIO
18 
+Imports:
19 
+    BiocBaseUtils,
20 
+    methods,
21 
+    S4Vectors,
22 
+    SpatialExperiment,
23 
+    VisiumIO
24 
+Suggests:
25 
+    arrow,
26 
+    BiocStyle,
27 
+    knitr,
28 
+    rmarkdown,
29 
+    tinytest
30 
+biocViews: Software, Infrastructure, DataImport, SingleCell, Spatial
31 
+VignetteBuilder: knitr
32 
+Encoding: UTF-8
33 
+Roxygen: list(markdown = TRUE)
34 
+RoxygenNote: 7.3.2
35 
+BugReports: https://github.com/waldronlab/XeniumIO/issues
36 
+URL: https://github.com/waldronlab/XeniumIO