1. scone
  2. DESCRIPTION
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Version bump

Davide Risso authored on 18/11/2022 17:12:17
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DESCRIPTION
History View file @ 701c577
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@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.23.0
2 
+Version: 1.23.1
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

Migrate from BatchJobs to batchtools following BiocParallel deprecation

Davide Risso authored on 18/11/2022 17:11:57
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DESCRIPTION
History View file @ 6d27294
... ... 
@@ -59,7 +59,7 @@ Suggests:
59 59 
   testthat,
60 60 
   visNetwork,
61 61 
   doParallel,
62 
-  BatchJobs,
62 
+  batchtools,
63 63 
   splatter,
64 64 
   scater,
65 65 
   kableExtra,
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:15:00
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DESCRIPTION
History View file @ ae134cc
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@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.22.0
2 
+Version: 1.23.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:15:00
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DESCRIPTION
History View file @ ce782b3
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.21.0
2 
+Version: 1.22.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:38:13
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DESCRIPTION
History View file @ ff3a800
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@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.20.0
2 
+Version: 1.21.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:38:13
Showing 1 changed files
DESCRIPTION
History View file @ eb71c4f
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@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.19.0
2 
+Version: 1.20.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 16:32:11
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DESCRIPTION
History View file @ 73bf4da
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.18.0
2 
+Version: 1.19.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 16:32:11
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DESCRIPTION
History View file @ 80329bd
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.17.2
2 
+Version: 1.18.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

Remove unneeded function import

Davide Risso authored on 16/09/2021 09:00:34
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DESCRIPTION
History View file @ 21cbec3
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.17.1
2 
+Version: 1.17.2
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
... ... 
@@ -79,5 +79,5 @@ biocViews:
79 79 
   SingleCell,
80 80 
   Coverage
81 81 
 BugReports: https://github.com/YosefLab/scone/issues
82 
-RoxygenNote: 7.1.1
82 
+RoxygenNote: 7.1.2
83 83 
 Encoding: UTF-8
Browse code

Remove Seurat dependency

Davide Risso authored on 07/07/2021 16:04:09
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DESCRIPTION
History View file @ 2d58c40
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@@ -64,7 +64,6 @@ Suggests:
64 64 
   scater,
65 65 
   kableExtra,
66 66 
   mclust,
67 
-  Seurat,
68 67 
   TENxPBMCData
69 68 
 VignetteBuilder: knitr
70 69 
 biocViews:
Browse code

Version bump

Davide Risso authored on 06/07/2021 16:29:54
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DESCRIPTION
History View file @ 36d376a
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@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.17.0
2 
+Version: 1.17.1
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

Update PsiNorm vignette

Davide Risso authored on 06/07/2021 16:27:16
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DESCRIPTION
History View file @ d9bb00b
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@@ -63,7 +63,9 @@ Suggests:
63 63 
   splatter,
64 64 
   scater,
65 65 
   kableExtra,
66 
-  mclust
66 
+  mclust,
67 
+  Seurat,
68 
+  TENxPBMCData
67 69 
 VignetteBuilder: knitr
68 70 
 biocViews:
69 71 
   ImmunoOncology,
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 16:25:07
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DESCRIPTION
History View file @ 2bcc746
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@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.16.0
2 
+Version: 1.17.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 16:25:07
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DESCRIPTION
History View file @ ad9c08b
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@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.15.2
2 
+Version: 1.16.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

Bump version

Davide Risso authored on 07/05/2021 08:26:12
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DESCRIPTION
History View file @ f12d5e6
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@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.15.1
2 
+Version: 1.15.2
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

Remove duplicate cluster dependency

Davide Risso authored on 06/05/2021 14:11:16
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DESCRIPTION
History View file @ d8443e6
... ... 
@@ -62,7 +62,6 @@ Suggests:
62 62 
   BatchJobs,
63 63 
   splatter,
64 64 
   scater,
65 
-  cluster,
66 65 
   kableExtra,
67 66 
   mclust
68 67 
 VignetteBuilder: knitr
Browse code

Remove lazy loading

Davide Risso authored on 06/05/2021 13:00:20
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DESCRIPTION
History View file @ 76db4ba
... ... 
@@ -66,7 +66,6 @@ Suggests:
66 66 
   kableExtra,
67 67 
   mclust
68 68 
 VignetteBuilder: knitr
69 
-LazyLoad: yes
70 69 
 biocViews:
71 70 
   ImmunoOncology,
72 71 
   Normalization,
Browse code

Bump version

Davide Risso authored on 06/05/2021 12:53:04
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DESCRIPTION
History View file @ 5c7b309
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.15.0
2 
+Version: 1.15.1
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

Add PsiNorm normalization

Davide Risso authored on 06/05/2021 10:59:52
Showing 1 changed files
DESCRIPTION
History View file @ a26bc47
... ... 
@@ -7,8 +7,12 @@ Description: SCONE is an R package for comparing and ranking the performance of
7 7 
 Authors@R: c(person("Michael", "Cole", email = "mbeloc@gmail.com",
8 8 
 	          role = c("aut", "cph")),
9 9 
 	     person("Davide", "Risso", email = "risso.davide@gmail.com",
10 
-	          role = c("aut", "cre", "cph")))
11 
-Maintainer: Davide Risso <risso.davide@gmail.com>
10 
+	          role = c("aut", "cre", "cph")),
11 
+	     person("Matteo", "Borella",
12 
+           email = "matteobor94@gmail.com",
13 
+           role = "ctb"),
14 
+           person("Chiara", "Romualdi", role = c("ctb"),
15 
+             email = "chiara.romualdi@gmail.com"))
12 16 
 License: Artistic-2.0
13 17 
 Depends:
14 18 
   R (>= 3.4),
... ... 
@@ -36,7 +40,9 @@ Imports:
36 40 
   boot,
37 41 
   rhdf5,
38 42 
   RUVSeq,
39 
-  rARPACK
43 
+  rARPACK,
44 
+  MatrixGenerics,
45 
+  SingleCellExperiment
40 46 
 Suggests:
41 47 
   BiocStyle,
42 48 
   DT,
... ... 
@@ -53,10 +59,16 @@ Suggests:
53 59 
   testthat,
54 60 
   visNetwork,
55 61 
   doParallel,
56 
-  BatchJobs
62 
+  BatchJobs,
63 
+  splatter,
64 
+  scater,
65 
+  cluster,
66 
+  kableExtra,
67 
+  mclust
57 68 
 VignetteBuilder: knitr
58 69 
 LazyLoad: yes
59 
-biocViews: ImmunoOncology,
70 
+biocViews:
71 
+  ImmunoOncology,
60 72 
   Normalization,
61 73 
   Preprocessing,
62 74 
   QualityControl,
... ... 
@@ -69,3 +81,4 @@ biocViews: ImmunoOncology,
69 81 
   Coverage
70 82 
 BugReports: https://github.com/YosefLab/scone/issues
71 83 
 RoxygenNote: 7.1.1
84 
+Encoding: UTF-8
Browse code

Update roxygen

Davide Risso authored on 06/05/2021 09:23:38
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DESCRIPTION
History View file @ 6deba0b
... ... 
@@ -68,4 +68,4 @@ biocViews: ImmunoOncology,
68 68 
   SingleCell,
69 69 
   Coverage
70 70 
 BugReports: https://github.com/YosefLab/scone/issues
71 
-RoxygenNote: 6.1.1
71 
+RoxygenNote: 7.1.1
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 15:20:29
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DESCRIPTION
History View file @ dcd4227
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.14.0
2 
+Version: 1.15.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 15:20:29
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DESCRIPTION
History View file @ 3fa8d6b
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.13.0
2 
+Version: 1.14.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 19:04:21
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DESCRIPTION
History View file @ 0521146
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.12.0
2 
+Version: 1.13.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 19:04:21
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DESCRIPTION
History View file @ a562a9e
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@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.11.1
2 
+Version: 1.12.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

Fix error due to change in scran

Davide Risso authored on 25/11/2019 17:40:59
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DESCRIPTION
History View file @ 83d07d5
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.11.0
2 
+Version: 1.11.1
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

bump x.y.z version to odd y after creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:42:12
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DESCRIPTION
History View file @ 268bee7
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.10.0
2 
+Version: 1.11.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:10:15
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DESCRIPTION
History View file @ 41dbdaf
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@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.9.2
2 
+Version: 1.10.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

Adding test dependencies as Suggests

Davide Risso authored on 07/10/2019 14:54:22
Showing 1 changed files
DESCRIPTION
History View file @ 82e9a90
... ... 
@@ -51,7 +51,9 @@ Suggests:
51 51 
   scRNAseq,
52 52 
   shiny,
53 53 
   testthat,
54 
-  visNetwork
54 
+  visNetwork,
55 
+  doParallel,
56 
+  BatchJobs
55 57 
 VignetteBuilder: knitr
56 58 
 LazyLoad: yes
57 59 
 biocViews: ImmunoOncology,
Browse code

Regenerate man pages

Davide Risso authored on 07/10/2019 14:18:05
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DESCRIPTION
History View file @ 57a48a9
... ... 
@@ -66,4 +66,4 @@ biocViews: ImmunoOncology,
66 66 
   SingleCell,
67 67 
   Coverage
68 68 
 BugReports: https://github.com/YosefLab/scone/issues
69 
-RoxygenNote: 6.0.1
69 
+RoxygenNote: 6.1.1
Browse code

Change maintainer

Davide Risso authored on 07/10/2019 14:14:10
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DESCRIPTION
History View file @ f036ea0
... ... 
@@ -5,11 +5,10 @@ Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
6 6 
 	high-throughput analyses.
7 7 
 Authors@R: c(person("Michael", "Cole", email = "mbeloc@gmail.com",
8 
-	          role = c("aut", "cre", "cph")),
8 
+	          role = c("aut", "cph")),
9 9 
 	     person("Davide", "Risso", email = "risso.davide@gmail.com",
10 
-	          role = c("aut", "cph")))
11 
-Author: Michael Cole [aut, cre, cph], Davide Risso [aut, cph]
12 
-Maintainer: Michael Cole <mbeloc@gmail.com>
10 
+	          role = c("aut", "cre", "cph")))
11 
+Maintainer: Davide Risso <risso.davide@gmail.com>
13 12 
 License: Artistic-2.0
14 13 
 Depends:
15 14 
   R (>= 3.4),
Browse code

Remove deprecation

Davide Risso authored on 07/10/2019 14:13:19
Showing 1 changed files
DESCRIPTION
History View file @ afcede6
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.9.1
2 
+Version: 1.9.2
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
... ... 
@@ -68,4 +68,3 @@ biocViews: ImmunoOncology,
68 68 
   Coverage
69 69 
 BugReports: https://github.com/YosefLab/scone/issues
70 70 
 RoxygenNote: 6.0.1
71 
-PackageStatus: Deprecated
Browse code

Package deprecation

lshep authored on 02/08/2019 14:19:37
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DESCRIPTION
History View file @ 3a7962e
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.9.0
2 
+Version: 1.9.1
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
... ... 
@@ -68,3 +68,4 @@ biocViews: ImmunoOncology,
68 68 
   Coverage
69 69 
 BugReports: https://github.com/YosefLab/scone/issues
70 70 
 RoxygenNote: 6.0.1
71 
+PackageStatus: Deprecated
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 16:14:04
Showing 1 changed files
DESCRIPTION
History View file @ 23c1e40
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.8.0
2 
+Version: 1.9.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 15:54:04
Showing 1 changed files
DESCRIPTION
History View file @ 4d72c47
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.7.1
2 
+Version: 1.8.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

Add ImmunoOncology biocViews term

Kayla-Morrell authored on 04/01/2019 18:48:53
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DESCRIPTION
History View file @ 56f9c5f
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.7.0
2 
+Version: 1.7.1
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
... ... 
@@ -55,7 +55,7 @@ Suggests:
55 55 
   visNetwork
56 56 
 VignetteBuilder: knitr
57 57 
 LazyLoad: yes
58 
-biocViews:
58 
+biocViews: ImmunoOncology,
59 59 
   Normalization,
60 60 
   Preprocessing,
61 61 
   QualityControl,
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:54:37
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DESCRIPTION
History View file @ 5bfbda6
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@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.6.0
2 
+Version: 1.7.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:42:03
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DESCRIPTION
History View file @ fbb3c96
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@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.5.1
2 
+Version: 1.6.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

replace BiocInstaller biocLite mentions with BiocManager

LiNk-NY authored on 30/08/2018 17:55:57
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DESCRIPTION
History View file @ 708baab
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@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.5.0
2 
+Version: 1.5.1
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:41:42
Showing 1 changed files
DESCRIPTION
History View file @ 6695ff4
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@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.4.0
2 
+Version: 1.5.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:35:44
Showing 1 changed files
DESCRIPTION
History View file @ 6360243
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.3.0
2 
+Version: 1.4.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:54:30
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DESCRIPTION
History View file @ e2436a3
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@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.2.0
2 
+Version: 1.3.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:41:24
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DESCRIPTION
History View file @ 49ae3d9
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.1.3
2 
+Version: 1.2.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

scone_1.1.3

mbcole authored on 19/10/2017 20:52:03
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DESCRIPTION
History View file @ af3da30
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.1.2-9001
2 
+Version: 1.1.3
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

Fix bug in shiny app

Davide Risso authored on 16/10/2017 15:17:51
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DESCRIPTION
History View file @ 37faf22
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.1.2
2 
+Version: 1.1.2-9001
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

Bump version for merge to master

Davide Risso authored on 03/07/2017 16:00:39
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DESCRIPTION
History View file @ cf2972f
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.1.1-99
2 
+Version: 1.1.2
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

remove EDASeq and scran dependencies

Davide Risso authored on 30/06/2017 22:14:15
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DESCRIPTION
History View file @ 0d72009
... ... 
@@ -25,8 +25,6 @@ Imports:
25 25 
   cluster,
26 26 
   compositions,
27 27 
   diptest,
28 
-  EDASeq,
29 
-  scran,
30 28 
   edgeR,
31 29 
   fpc,
32 30 
   gplots,
... ... 
@@ -50,6 +48,7 @@ Suggests:
50 48 
   plotly,
51 49 
   reshape2,
52 50 
   rmarkdown,
51 
+  scran,
53 52 
   scRNAseq,
54 53 
   shiny,
55 54 
   testthat,
Browse code

Shiny app packages to Suggests:

Davide Risso authored on 30/06/2017 21:47:09
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DESCRIPTION
History View file @ d415a9d
... ... 
@@ -39,21 +39,21 @@ Imports:
39 39 
   boot,
40 40 
   rhdf5,
41 41 
   RUVSeq,
42 
-  DT,
43 
-  NMF,
44 
-  ggplot2,
45 
-  plotly,
46 
-  reshape2,
47 
-  visNetwork,
48 42 
   rARPACK
49 43 
 Suggests:
50 44 
   BiocStyle,
45 
+  DT,
46 
+  ggplot2,
51 47 
   knitr,
52 48 
   miniUI,
49 
+  NMF,
50 
+  plotly,
51 
+  reshape2,
53 52 
   rmarkdown,
54 53 
   scRNAseq,
55 54 
   shiny,
56 
-  testthat
55 
+  testthat,
56 
+  visNetwork
57 57 
 VignetteBuilder: knitr
58 58 
 LazyLoad: yes
59 59 
 biocViews:
Browse code

shiny and miniUI in Suggests:

Davide Risso authored on 30/06/2017 21:29:49
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DESCRIPTION
History View file @ 3a7e0cb
... ... 
@@ -37,8 +37,6 @@ Imports:
37 37 
   mixtools,
38 38 
   RColorBrewer,
39 39 
   boot,
40 
-  shiny,
41 
-  miniUI,
42 40 
   rhdf5,
43 41 
   RUVSeq,
44 42 
   DT,
... ... 
@@ -50,9 +48,11 @@ Imports:
50 48 
   rARPACK
51 49 
 Suggests:
52 50 
   BiocStyle,
53 
-  scRNAseq,
54 51 
   knitr,
52 
+  miniUI,
55 53 
   rmarkdown,
54 
+  scRNAseq,
55 
+  shiny,
56 56 
   testthat
57 57 
 VignetteBuilder: knitr
58 58 
 LazyLoad: yes
Browse code

Bump version for develop

Davide Risso authored on 30/06/2017 21:22:18
Showing 1 changed files
DESCRIPTION
History View file @ 9655443
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.1.1
2 
+Version: 1.1.1-99
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

Back to R 3.4 (for merge with bioc)

Davide Risso authored on 30/06/2017 20:20:12
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DESCRIPTION
History View file @ 3f36731
... ... 
@@ -12,7 +12,7 @@ Author: Michael Cole [aut, cre, cph], Davide Risso [aut, cph]
12 12 
 Maintainer: Michael Cole <mbeloc@gmail.com>
13 13 
 License: Artistic-2.0
14 14 
 Depends:
15 
-  R (>= 3.3),
15 
+  R (>= 3.4),
16 16 
   methods,
17 17 
   SummarizedExperiment
18 18 
 Imports:
Browse code

NEWS and version bump

Davide Risso authored on 30/06/2017 20:19:06
Showing 1 changed files
DESCRIPTION
History View file @ 9b88f6d
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 0.99.7
2 
+Version: 1.1.1
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

Merge branch 'develop'

Davide Risso authored on 30/06/2017 20:14:32
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Browse code

Change version

Davide Risso authored on 07/04/2017 01:46:03
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DESCRIPTION
History View file @ 773b583
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 1.0.0
2 
+Version: 0.99.7
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

Version 3.3

mbcole authored on 06/04/2017 23:17:22
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DESCRIPTION
History View file @ a775a85
... ... 
@@ -12,7 +12,7 @@ Author: Michael Cole [aut, cre, cph], Davide Risso [aut, cph]
12 12 
 Maintainer: Michael Cole <mbeloc@gmail.com>
13 13 
 License: Artistic-2.0
14 14 
 Depends:
15 
-  R (>= 3.4),
15 
+  R (>= 3.3),
16 16 
   methods,
17 17 
   SummarizedExperiment
18 18 
 Imports:
Browse code

Description R version and NEWS

mbcole authored on 06/04/2017 23:10:20
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DESCRIPTION
History View file @ aa76059
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 0.99.6
2 
+Version: 1.0.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
... ... 
@@ -12,7 +12,7 @@ Author: Michael Cole [aut, cre, cph], Davide Risso [aut, cph]
12 12 
 Maintainer: Michael Cole <mbeloc@gmail.com>
13 13 
 License: Artistic-2.0
14 14 
 Depends:
15 
-  R (>= 3.3),
15 
+  R (>= 3.4),
16 16 
   methods,
17 17 
   SummarizedExperiment
18 18 
 Imports:
Browse code

Added scran wrapper

mbcole authored on 05/04/2017 20:33:49
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DESCRIPTION
History View file @ 1302a82
... ... 
@@ -26,6 +26,7 @@ Imports:
26 26 
   compositions,
27 27 
   diptest,
28 28 
   EDASeq,
29 
+  scran,
29 30 
   edgeR,
30 31 
   fpc,
31 32 
   gplots,
Browse code

Added compositions removed DESEq

mbcole authored on 05/04/2017 19:27:37
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DESCRIPTION
History View file @ 87bfea8
... ... 
@@ -23,7 +23,7 @@ Imports:
23 23 
   BiocParallel,
24 24 
   class,
25 25 
   cluster,
26 
-  DESeq,
26 
+  compositions,
27 27 
   diptest,
28 28 
   EDASeq,
29 29 
   edgeR,
Browse code

Updated documentation

mbcole authored on 04/04/2017 21:37:54
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DESCRIPTION
History View file @ fa8db85
... ... 
@@ -67,4 +67,4 @@ biocViews:
67 67 
   SingleCell,
68 68 
   Coverage
69 69 
 BugReports: https://github.com/YosefLab/scone/issues
70 
-RoxygenNote: 5.0.1
70 
+RoxygenNote: 6.0.1
Browse code

Merge with bioc submission

mbcole authored on 10/01/2017 00:14:56
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Browse code

Modified documentation, more examples and exported getters, added links between SconeExperiment and methods, and apply getters to setValidate

mbcole authored on 14/12/2016 00:54:28
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DESCRIPTION
History View file @ 53885e4
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 0.99.5
2 
+Version: 0.99.6
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

Removed html of vignette

Davide Risso authored on 01/12/2016 18:10:37
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DESCRIPTION
History View file @ 017e0dc
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 0.99.4
2 
+Version: 0.99.5
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

Merge functional (R > 3.3) master into develop

mbcole authored on 29/11/2016 01:38:16
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Browse code

Version bump

Davide Risso authored on 23/11/2016 18:50:10
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DESCRIPTION
History View file @ 13b31a4
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 0.99.3
2 
+Version: 0.99.4
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
Browse code

Change to require 3.4 and bump version

mbcole authored on 22/11/2016 23:22:25
Showing 1 changed files
DESCRIPTION
History View file @ 8961901
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 0.99.2
2 
+Version: 0.99.3
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of
5 5 
 	different normalization schemes for single-cell RNA-seq and other
... ... 
@@ -12,7 +12,7 @@ Author: Michael Cole [aut, cre, cph], Davide Risso [aut, cph]
12 12 
 Maintainer: Michael Cole <mbeloc@gmail.com>
13 13 
 License: Artistic-2.0
14 14 
 Depends:
15 
-  R (>= 3.3),
15 
+  R (>= 3.4),
16 16 
   methods,
17 17 
   SummarizedExperiment
18 18 
 Imports:
Browse code

Reformat lines and fixed bugs in easy wrapper

mbcole authored on 22/11/2016 22:48:59
Showing 1 changed files
DESCRIPTION
History View file @ c9cd07e
... ... 
@@ -1,7 +1,9 @@
1 1 
 Package: scone
2 2 
 Version: 0.99.2
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 
-Description: SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.
4 
+Description: SCONE is an R package for comparing and ranking the performance of
5 
+	different normalization schemes for single-cell RNA-seq and other
6 
+	high-throughput analyses.
5 7 
 Authors@R: c(person("Michael", "Cole", email = "mbeloc@gmail.com",
6 8 
 	          role = c("aut", "cre", "cph")),
7 9 
 	     person("Davide", "Risso", email = "risso.davide@gmail.com",
... ... 
@@ -43,7 +45,6 @@ Imports:
43 45 
   ggplot2,
44 46 
   plotly,
45 47 
   reshape2,
46 
-  scran,
47 48 
   visNetwork
48 49 
 Suggests:
49 50 
   BiocStyle,
... ... 
@@ -60,6 +61,9 @@ biocViews:
60 61 
   GeneExpression,
61 62 
   RNASeq,
62 63 
   Software,
63 
-  Transcriptomics
64 
+  Transcriptomics,
65 
+  Sequencing,
66 
+  SingleCell,
67 
+  Coverage
64 68 
 BugReports: https://github.com/YosefLab/scone/issues
65 69 
 RoxygenNote: 5.0.1
Browse code

Faster svd with rARPACK

Davide Risso authored on 18/11/2016 00:38:50
Showing 1 changed files
DESCRIPTION
History View file @ f4cbf2b
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 0.99.2
2 
+Version: 0.99.2-9000
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.
5 5 
 Authors@R: c(person("Michael", "Cole", email = "mbeloc@gmail.com",
... ... 
@@ -44,7 +44,8 @@ Imports:
44 44 
   plotly,
45 45 
   reshape2,
46 46 
   scran,
47 
-  visNetwork
47 
+  visNetwork,
48 
+  rARPACK
48 49 
 Suggests:
49 50 
   BiocStyle,
50 51 
   scRNAseq,
Browse code

Fixed back-end for Windows (again)

Davide Risso authored on 16/11/2016 18:47:58
Showing 1 changed files
DESCRIPTION
History View file @ 372df0e
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 0.99.1
2 
+Version: 0.99.2
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.
5 5 
 Authors@R: c(person("Michael", "Cole", email = "mbeloc@gmail.com",
Browse code

Correct vignette engine

Davide Risso authored on 15/11/2016 19:02:48
Showing 1 changed files
DESCRIPTION
History View file @ 5d3f3bb
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 0.99.0
2 
+Version: 0.99.1
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.
5 5 
 Authors@R: c(person("Michael", "Cole", email = "mbeloc@gmail.com",
Browse code

Artistic 2.0

mbcole authored on 14/11/2016 23:41:55
Showing 1 changed files
DESCRIPTION
History View file @ b1931f1
... ... 
@@ -8,7 +8,7 @@ Authors@R: c(person("Michael", "Cole", email = "mbeloc@gmail.com",
8 8 
 	          role = c("aut", "cph")))
9 9 
 Author: Michael Cole [aut, cre, cph], Davide Risso [aut, cph]
10 10 
 Maintainer: Michael Cole <mbeloc@gmail.com>
11 
-License: file LICENSE
11 
+License: Artistic-2.0
12 12 
 Depends:
13 13 
   R (>= 3.3),
14 14 
   methods,
Browse code

Updated doumentations and S4 interface fixes

mbcole authored on 14/11/2016 22:31:36
Showing 1 changed files
DESCRIPTION
History View file @ e9aed5e
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 0.0.99-9002
2 
+Version: 0.99.0
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.
5 5 
 Authors@R: c(person("Michael", "Cole", email = "mbeloc@gmail.com",
... ... 
@@ -14,6 +14,9 @@ Depends:
14 14 
   methods,
15 15 
   SummarizedExperiment
16 16 
 Imports:
17 
+  graphics,
18 
+  stats,
19 
+  utils,
17 20 
   aroma.light,
18 21 
   BiocParallel,
19 22 
   class,
... ... 
@@ -50,5 +53,13 @@ Suggests:
50 53 
   testthat
51 54 
 VignetteBuilder: knitr
52 55 
 LazyLoad: yes
56 
+biocViews:
57 
+  Normalization,
58 
+  Preprocessing,
59 
+  QualityControl,
60 
+  GeneExpression,
61 
+  RNASeq,
62 
+  Software,
63 
+  Transcriptomics
53 64 
 BugReports: https://github.com/YosefLab/scone/issues
54 65 
 RoxygenNote: 5.0.1
Browse code

Remove zinb functions

Davide Risso authored on 04/11/2016 23:55:09
Showing 1 changed files
DESCRIPTION
History View file @ 8cbe329
... ... 
@@ -27,7 +27,6 @@ Imports:
27 27 
   grDevices,
28 28 
   hexbin,
29 29 
   limma,
30 
-  MASS,
31 30 
   matrixStats,
32 31 
   mixtools,
33 32 
   RColorBrewer,
Browse code

Add scran to Imports:

Davide Risso authored on 04/11/2016 23:51:04
Showing 1 changed files
DESCRIPTION
History View file @ 3645de4
... ... 
@@ -41,6 +41,7 @@ Imports:
41 41 
   ggplot2,
42 42 
   plotly,
43 43 
   reshape2,
44 
+  scran,
44 45 
   visNetwork
45 46 
 Suggests:
46 47 
   BiocStyle,
Browse code

Added scRNAseq for vignette building

Davide Risso authored on 04/11/2016 21:55:43
Showing 1 changed files
DESCRIPTION
History View file @ 7abc5f4
... ... 
@@ -44,6 +44,7 @@ Imports:
44 44 
   visNetwork
45 45 
 Suggests:
46 46 
   BiocStyle,
47 
+  scRNAseq,
47 48 
   knitr,
48 49 
   rmarkdown,
49 50 
   testthat
Browse code

Added BiocStyle for vignette building

Davide Risso authored on 04/11/2016 21:51:50
Showing 1 changed files
DESCRIPTION
History View file @ 0c41917
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 0.0.99-9001
2 
+Version: 0.0.99-9002
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.
5 5 
 Authors@R: c(person("Michael", "Cole", email = "mbeloc@gmail.com",
... ... 
@@ -43,6 +43,7 @@ Imports:
43 43 
   reshape2,
44 44 
   visNetwork
45 45 
 Suggests:
46 
+  BiocStyle,
46 47 
   knitr,
47 48 
   rmarkdown,
48 49 
   testthat
Browse code

Update NEWS

Davide Risso authored on 07/10/2016 23:24:46
Showing 1 changed files
DESCRIPTION
History View file @ d7db527
... ... 
@@ -8,7 +8,6 @@ Authors@R: c(person("Michael", "Cole", email = "mbeloc@gmail.com",
8 8 
 	          role = c("aut", "cph")))
9 9 
 Author: Michael Cole [aut, cre, cph], Davide Risso [aut, cph]
10 10 
 Maintainer: Michael Cole <mbeloc@gmail.com>
11 
-Date: 2016-09-26
12 11 
 License: file LICENSE
13 12 
 Depends:
14 13 
   R (>= 3.3),
Browse code

Depend on SummarizedExperiment

Davide Risso authored on 28/09/2016 17:21:53
Showing 1 changed files
DESCRIPTION
History View file @ cc75346
... ... 
@@ -12,7 +12,8 @@ Date: 2016-09-26
12 12 
 License: file LICENSE
13 13 
 Depends:
14 14 
   R (>= 3.3),
15 
-  methods
15 
+  methods,
16 
+  SummarizedExperiment
16 17 
 Imports:
17 18 
   aroma.light,
18 19 
   BiocParallel,
... ... 
@@ -41,8 +42,7 @@ Imports:
41 42 
   ggplot2,
42 43 
   plotly,
43 44 
   reshape2,
44 
-  visNetwork,
45 
-  SummarizedExperiment
45 
+  visNetwork
46 46 
 Suggests:
47 47 
   knitr,
48 48 
   rmarkdown,
Browse code

First attempt at creating scone class

Davide Risso authored on 27/09/2016 18:47:30
Showing 1 changed files
DESCRIPTION
History View file @ 4b6fc70
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: scone
2 
-Version: 0.0.8-9000
2 
+Version: 0.0.99-9001
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 4 
 Description: SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.
5 5 
 Authors@R: c(person("Michael", "Cole", email = "mbeloc@gmail.com",
... ... 
@@ -11,7 +11,8 @@ Maintainer: Michael Cole <mbeloc@gmail.com>
11 11 
 Date: 2016-09-26
12 12 
 License: file LICENSE
13 13 
 Depends:
14 
-  R (>= 3.3)
14 
+  R (>= 3.3),
15 
+  methods
15 16 
 Imports:
16 17 
   aroma.light,
17 18 
   BiocParallel,
... ... 
@@ -40,7 +41,8 @@ Imports:
40 41 
   ggplot2,
41 42 
   plotly,
42 43 
   reshape2,
43 
-  visNetwork
44 
+  visNetwork,
45 
+  SummarizedExperiment
44 46 
 Suggests:
45 47 
   knitr,
46 48 
   rmarkdown,
Browse code

Version Notes and Bump

mbcole authored on 26/09/2016 17:52:07
Showing 1 changed files
DESCRIPTION
History View file @ db2d58e
... ... 
@@ -1,14 +1,14 @@
1 1 
 Package: scone
2 
-Version: 0.0.7-9000
2 
+Version: 0.0.8-9000
3 3 
 Title: Single Cell Overview of Normalized Expression data
4 
-Description: scone is a package to compare and rank the performance of different normalization schemes in real single-cell RNA-seq datasets.
4 
+Description: SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.
5 5 
 Authors@R: c(person("Michael", "Cole", email = "mbeloc@gmail.com",
6 6 
 	          role = c("aut", "cre", "cph")),
7 7 
 	     person("Davide", "Risso", email = "risso.davide@gmail.com",
8 8 
 	          role = c("aut", "cph")))
9 9 
 Author: Michael Cole [aut, cre, cph], Davide Risso [aut, cph]
10 10 
 Maintainer: Michael Cole <mbeloc@gmail.com>
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-Date: 2016-07-22
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+Date: 2016-09-26
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 License: file LICENSE
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 Depends:
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   R (>= 3.3)
Browse code

Added SCONE Report Function, Fixed RLE_IQR metric, and Changed Mean Score to Mean Score Rank to avoidmetric-dependent variances.

mbcole authored on 26/09/2016 07:17:49
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DESCRIPTION
History View file @ d9a7803
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@@ -34,7 +34,13 @@ Imports:
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   shiny,
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   miniUI,
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   rhdf5,
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-  RUVSeq
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+  RUVSeq,
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+  DT,
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+  NMF,
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+  ggplot2,
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+  plotly,
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+  reshape2,
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+  visNetwork
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 Suggests:
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   knitr,
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   rmarkdown,
Browse code

Merge branch 'hotfix_license' into develop

allonw authored on 08/08/2016 21:26:11
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hotfix: changed license by Nir's request

allonw authored on 08/08/2016 21:25:18
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@@ -9,7 +9,7 @@ Authors@R: c(person("Michael", "Cole", email = "mbeloc@gmail.com",
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 Author: Michael Cole [aut, cre, cph], Davide Risso [aut, cph]
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 Maintainer: Michael Cole <mbeloc@gmail.com>
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 Date: 2016-07-22
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-License: Artistic-2.0
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+License: file LICENSE
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 Depends:
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   R (>= 3.3)
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 Imports:
Browse code

Revert "changed license by nir's request" in order to do in a new branch and hotfix master immediately

This reverts commit 43a89a7ee4c52e1511a6296ca534c86604326354.

allonw authored on 08/08/2016 21:11:18
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@@ -9,7 +9,7 @@ Authors@R: c(person("Michael", "Cole", email = "mbeloc@gmail.com",
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 Author: Michael Cole [aut, cre, cph], Davide Risso [aut, cph]
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 Maintainer: Michael Cole <mbeloc@gmail.com>
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 Date: 2016-07-22
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-License: file LICENSE
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+License: Artistic-2.0
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 Depends:
14 14 
   R (>= 3.3)
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 Imports:
Browse code

changed license by nir's request

allonw authored on 08/08/2016 19:59:58
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DESCRIPTION
History View file @ 43a89a7
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@@ -9,7 +9,7 @@ Authors@R: c(person("Michael", "Cole", email = "mbeloc@gmail.com",
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 Author: Michael Cole [aut, cre, cph], Davide Risso [aut, cph]
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