1. epihet
  2. DESCRIPTION
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bump x.y.z version to odd y following creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:18:59
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 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 
-Version: 1.14.0
3 
+Version: 1.15.0
4 4 
 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
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     email = "Xiaowen.Chen@jax.org"),
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     person("Haitham", "Ashoor",role = "aut"),
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bump x.y.z version to even y prior to creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:18:59
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1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 
-Version: 1.13.0
3 
+Version: 1.14.0
4 4 
 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 5 
     email = "Xiaowen.Chen@jax.org"),
6 6 
     person("Haitham", "Ashoor",role = "aut"),
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bump x.y.z version to odd y following creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:52:29
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1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 
-Version: 1.12.0
3 
+Version: 1.13.0
4 4 
 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 5 
     email = "Xiaowen.Chen@jax.org"),
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     person("Haitham", "Ashoor",role = "aut"),
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bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:52:29
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 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 
-Version: 1.11.1
3 
+Version: 1.12.0
4 4 
 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 5 
     email = "Xiaowen.Chen@jax.org"),
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     person("Haitham", "Ashoor",role = "aut"),
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Pass serialized GRanges object thru updateObject()

Hervé Pagès authored on 19/11/2021 01:22:56
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1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 
-Version: 1.11.0
3 
+Version: 1.11.1
4 4 
 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 5 
     email = "Xiaowen.Chen@jax.org"),
6 6 
     person("Haitham", "Ashoor",role = "aut"),
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bump x.y.z version to odd y following creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 16:48:37
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1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 
-Version: 1.10.0
3 
+Version: 1.11.0
4 4 
 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 5 
     email = "Xiaowen.Chen@jax.org"),
6 6 
     person("Haitham", "Ashoor",role = "aut"),
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bump x.y.z version to even y prior to creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 16:48:37
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1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 
-Version: 1.9.0
3 
+Version: 1.10.0
4 4 
 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 5 
     email = "Xiaowen.Chen@jax.org"),
6 6 
     person("Haitham", "Ashoor",role = "aut"),
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bump x.y.z version to odd y following creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 16:39:58
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1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 
-Version: 1.8.0
3 
+Version: 1.9.0
4 4 
 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 5 
     email = "Xiaowen.Chen@jax.org"),
6 6 
     person("Haitham", "Ashoor",role = "aut"),
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bump x.y.z version to even y prior to creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 16:39:58
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DESCRIPTION
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1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 
-Version: 1.7.1
3 
+Version: 1.8.0
4 4 
 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 5 
     email = "Xiaowen.Chen@jax.org"),
6 6 
     person("Haitham", "Ashoor",role = "aut"),
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Update DESCRIPTION

xiaowen chen authored on 25/11/2020 00:10:17 • GitHub committed on 25/11/2020 00:10:17
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History View file @553ed09
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1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 
-Version: 1.8.0
3 
+Version: 1.7.1
4 4 
 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 5 
     email = "Xiaowen.Chen@jax.org"),
6 6 
     person("Haitham", "Ashoor",role = "aut"),
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Update DESCRIPTION

xiaowen chen authored on 24/11/2020 23:57:17 • GitHub committed on 24/11/2020 23:57:17
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1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
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-Version: 1.7.2
3 
+Version: 1.8.0
4 4 
 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 5 
     email = "Xiaowen.Chen@jax.org"),
6 6 
     person("Haitham", "Ashoor",role = "aut"),
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Update DESCRIPTION

xiaowen chen authored on 24/11/2020 23:52:42 • GitHub committed on 24/11/2020 23:52:42
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1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 
-Version: 1.5.5
3 
+Version: 1.7.2
4 4 
 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 5 
     email = "Xiaowen.Chen@jax.org"),
6 6 
     person("Haitham", "Ashoor",role = "aut"),
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Update DESCRIPTION

xiaowen chen authored on 26/10/2020 20:13:52 • GitHub committed on 26/10/2020 20:13:52
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1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 
-Version: 1.5.4
3 
+Version: 1.5.5
4 4 
 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 5 
     email = "Xiaowen.Chen@jax.org"),
6 6 
     person("Haitham", "Ashoor",role = "aut"),
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Update DESCRIPTION

xiaowen chen authored on 20/10/2020 23:54:47 • GitHub committed on 20/10/2020 23:54:47
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@@ -1,6 +1,6 @@
1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 
-Version: 1.5.3
3 
+Version: 1.5.4
4 4 
 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 5 
     email = "Xiaowen.Chen@jax.org"),
6 6 
     person("Haitham", "Ashoor",role = "aut"),
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Update DESCRIPTION

xiaowen chen authored on 17/10/2020 18:41:01 • GitHub committed on 17/10/2020 18:41:01
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@@ -1,6 +1,6 @@
1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 
-Version: 1.5.2
3 
+Version: 1.5.3
4 4 
 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 5 
     email = "Xiaowen.Chen@jax.org"),
6 6 
     person("Haitham", "Ashoor",role = "aut"),
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Update DESCRIPTION

xiaowen chen authored on 14/10/2020 14:39:45 • GitHub committed on 14/10/2020 14:39:45
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@@ -1,6 +1,6 @@
1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 
-Version: 1.5.1
3 
+Version: 1.5.2
4 4 
 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 5 
     email = "Xiaowen.Chen@jax.org"),
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     person("Haitham", "Ashoor",role = "aut"),
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Update DESCRIPTION

xiaowen chen authored on 29/09/2020 00:11:17 • GitHub committed on 29/09/2020 00:11:17
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@@ -1,6 +1,6 @@
1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 
-Version: 1.5.0
3 
+Version: 1.5.1
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 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 5 
     email = "Xiaowen.Chen@jax.org"),
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     person("Haitham", "Ashoor",role = "aut"),
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bump x.y.z version to odd y following creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 19:22:09
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@@ -1,6 +1,6 @@
1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 
-Version: 1.4.0
3 
+Version: 1.5.0
4 4 
 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 5 
     email = "Xiaowen.Chen@jax.org"),
6 6 
     person("Haitham", "Ashoor",role = "aut"),
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bump x.y.z version to even y prior to creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 19:22:09
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DESCRIPTION
History View file @f510661
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1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 
-Version: 1.3.0
3 
+Version: 1.4.0
4 4 
 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 5 
     email = "Xiaowen.Chen@jax.org"),
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     person("Haitham", "Ashoor",role = "aut"),
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bump x.y.z version to odd y after creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:43:23
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1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
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-Version: 1.2.0
3 
+Version: 1.3.0
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 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 5 
     email = "Xiaowen.Chen@jax.org"),
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     person("Haitham", "Ashoor",role = "aut"),
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bump x.y.z version to even y prior to creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:11:28
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1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
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-Version: 1.1.0
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+Version: 1.2.0
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 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 5 
     email = "Xiaowen.Chen@jax.org"),
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     person("Haitham", "Ashoor",role = "aut"),
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bump x.y.z versions to odd y after creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 16:16:19
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1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
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-Version: 1.0.0
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+Version: 1.1.0
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 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
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     email = "Xiaowen.Chen@jax.org"),
6 6 
     person("Haitham", "Ashoor",role = "aut"),
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bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 15:54:14
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History View file @19d2d7d
1 1 
old mode 100755
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new mode 100644
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1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
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-Version: 0.99.9
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+Version: 1.0.0
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 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
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     email = "Xiaowen.Chen@jax.org"),
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     person("Haitham", "Ashoor",role = "aut"),
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Fix poorly formatted NEWS file

lshep authored on 22/04/2019 13:19:01
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@@ -1,6 +1,6 @@
1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 
-Version: 0.99.8
3 
+Version: 0.99.9
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 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 5 
     email = "Xiaowen.Chen@jax.org"),
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     person("Haitham", "Ashoor",role = "aut"),
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Update DESCRIPTION

xiaowen chen authored on 04/12/2018 16:54:22 • GitHub committed on 04/12/2018 16:54:22
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1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
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-Version: 0.99.7
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+Version: 0.99.8
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 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
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     email = "Xiaowen.Chen@jax.org"),
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     person("Haitham", "Ashoor",role = "aut"),
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revised according to bioconductor review

Mingsheng Zhang authored on 03/12/2018 02:17:44
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@@ -1,6 +1,6 @@
1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
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-Version: 0.99.6
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+Version: 0.99.7
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 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
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     email = "Xiaowen.Chen@jax.org"),
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     person("Haitham", "Ashoor",role = "aut"),
... ... 
@@ -19,7 +19,7 @@ Description: epihet is an R-package that calculates the epigenetic
19 19 
     created by calculating the differential heterogeneity of the samples.
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     And we construct co-epihet network and perform network analysis.
21 21 
 Depends:
22 
-    R(>= 3.4.1),
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+    R(>= 3.6),
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     GenomicRanges,
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     IRanges,
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     S4Vectors,
Browse code

modify compMatrix, DiffHet, epiBox, epiMap. reverse DESCRIPTION, NAMESPACE

Mingsheng Zhang authored on 30/11/2018 21:05:51
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DESCRIPTION
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@@ -43,7 +43,7 @@ Imports:
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     WGCNA,
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     ReactomePA
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 Encoding: UTF-8
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-RoxygenNote: 6.1.1
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+RoxygenNote: 6.0.1
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 Suggests:
48 48 
     knitr,
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     clusterProfiler,
Browse code

modify data.R

Mingsheng Zhang authored on 30/11/2018 19:18:30
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DESCRIPTION
History View file @dc4f7ef
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@@ -19,7 +19,7 @@ Description: epihet is an R-package that calculates the epigenetic
19 19 
     created by calculating the differential heterogeneity of the samples.
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     And we construct co-epihet network and perform network analysis.
21 21 
 Depends:
22 
-    R(>= 3.6),
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+    R(>= 3.4.1),
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     GenomicRanges,
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     IRanges,
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     S4Vectors,
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@@ -43,7 +43,7 @@ Imports:
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     WGCNA,
44 44 
     ReactomePA
45 45 
 Encoding: UTF-8
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-RoxygenNote: 6.0.1
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+RoxygenNote: 6.1.1
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 Suggests:
48 48 
     knitr,
49 49 
     clusterProfiler,
Browse code

Update DESCRIPTION

xiaowen chen authored on 28/11/2018 00:17:21 • GitHub committed on 28/11/2018 00:17:21
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DESCRIPTION
History View file @1c661f7
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@@ -1,6 +1,6 @@
1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 
-Version: 0.99.5
3 
+Version: 0.99.6
4 4 
 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 5 
     email = "Xiaowen.Chen@jax.org"),
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     person("Haitham", "Ashoor",role = "aut"),
... ... 
@@ -19,7 +19,7 @@ Description: epihet is an R-package that calculates the epigenetic
19 19 
     created by calculating the differential heterogeneity of the samples.
20 20 
     And we construct co-epihet network and perform network analysis.
21 21 
 Depends:
22 
-    R(>= 3.5.1),
22 
+    R(>= 3.6),
23 23 
     GenomicRanges,
24 24 
     IRanges,
25 25 
     S4Vectors,
Browse code

revised epihet.Rnw, build/check succeeded. Change R to 3.5.1 in DESCRIPTION.

Mingsheng Zhang authored on 26/11/2018 02:15:40
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DESCRIPTION
History View file @0f0059e
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@@ -1,10 +1,11 @@
1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 
-Version: 0.99.4
3 
+Version: 0.99.5
4 4 
 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 5 
     email = "Xiaowen.Chen@jax.org"),
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     person("Haitham", "Ashoor",role = "aut"),
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     person("Ryan", "Musich", role = "aut"),
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+    person("Mingsheng","Zhang",role="aut"),
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     person("Jiahui","Wang",role = "aut"),
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     person("Sheng", "Li", role = "aut"))
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 Description: epihet is an R-package that calculates the epigenetic
... ... 
@@ -18,7 +19,7 @@ Description: epihet is an R-package that calculates the epigenetic
18 19 
     created by calculating the differential heterogeneity of the samples.
19 20 
     And we construct co-epihet network and perform network analysis.
20 21 
 Depends:
21 
-    R(>= 3.4.1),
22 
+    R(>= 3.5.1),
22 23 
     GenomicRanges,
23 24 
     IRanges,
24 25 
     S4Vectors,
Browse code

change package name from EpiHet to epihet

Mingsheng Zhang authored on 20/11/2018 14:14:36
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DESCRIPTION
History View file @c4f3d49
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@@ -1,4 +1,4 @@
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-Package: EpiHet
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+Package: epihet
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 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
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 Version: 0.99.4
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 Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
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@@ -7,13 +7,13 @@ Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
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     person("Ryan", "Musich", role = "aut"),
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     person("Jiahui","Wang",role = "aut"),
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     person("Sheng", "Li", role = "aut"))
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-Description: EpiHet is an R-package that calculates the epigenetic
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+Description: epihet is an R-package that calculates the epigenetic
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     heterogeneity between cancer cells and/or normal cells. The functions
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     establish a pipeline that take in bisulfite sequencing data from multiple
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     samples and use the data to track similarities and differences in
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     epipolymorphism,proportion of discordantly methylated sequencing reads
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     (PDR),and Shannon entropy values at epialleles that are shared between
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-    the samples.EpiHet can be used to perform analysis on the data by creating
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+    the samples.epihet can be used to perform analysis on the data by creating
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     pheatmaps, box plots, PCA plots, and t-SNE plots. MA plots can also be
18 18 
     created by calculating the differential heterogeneity of the samples.
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     And we construct co-epihet network and perform network analysis.
... ... 
@@ -42,7 +42,7 @@ Imports:
42 42 
     WGCNA,
43 43 
     ReactomePA
44 44 
 Encoding: UTF-8
45 
-RoxygenNote: 6.1.1
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+RoxygenNote: 6.0.1
46 46 
 Suggests:
47 47 
     knitr,
48 48 
     clusterProfiler,
Browse code

rerun roxygen

Mingsheng Zhang authored on 20/11/2018 01:59:38
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DESCRIPTION
History View file @6c49d13
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@@ -42,7 +42,7 @@ Imports:
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     WGCNA,
43 43 
     ReactomePA
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 Encoding: UTF-8
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-RoxygenNote: 6.0.1
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+RoxygenNote: 6.1.1
46 46 
 Suggests:
47 47 
     knitr,
48 48 
     clusterProfiler,
Browse code

checked DESCRIPYION, R/data.R

Mingsheng Zhang authored on 19/11/2018 22:58:04
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DESCRIPTION
History View file @b812098
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@@ -1,38 +1,55 @@
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-Package: epihet
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+Package: EpiHet
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 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
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-Date: 2018-04-10
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-Version: 0.99.3
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-Authors@R: c(person("Xiaowen", "Chen", email = "Xiaowen.Chen@jax.org",
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-    role = c("aut", "cre")),person("Haitham", "Ashoor",
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-    role = c("aut")),person("Ryan", "Musich", role = c("aut")),
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-    person("Jiahui","Wang",role = "aut"),person("Sheng", "Li", role = "aut"))
9 
-Description: epihet is an R-package that calculates the epigenetic
3 
+Version: 0.99.4
4 
+Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
5 
+    email = "Xiaowen.Chen@jax.org"),
6 
+    person("Haitham", "Ashoor",role = "aut"),
7 
+    person("Ryan", "Musich", role = "aut"),
8 
+    person("Jiahui","Wang",role = "aut"),
9 
+    person("Sheng", "Li", role = "aut"))
10 
+Description: EpiHet is an R-package that calculates the epigenetic
10 11 
     heterogeneity between cancer cells and/or normal cells. The functions
11 12 
     establish a pipeline that take in bisulfite sequencing data from multiple
12 13 
     samples and use the data to track similarities and differences in
13 14 
     epipolymorphism,proportion of discordantly methylated sequencing reads
14 15 
     (PDR),and Shannon entropy values at epialleles that are shared between
15 
-    the samples.epihet can be used to perform analysis on the data by creating
16 
+    the samples.EpiHet can be used to perform analysis on the data by creating
16 17 
     pheatmaps, box plots, PCA plots, and t-SNE plots. MA plots can also be
17 18 
     created by calculating the differential heterogeneity of the samples.
18 19 
     And we construct co-epihet network and perform network analysis.
19 20 
 Depends:
20 
-    R(>= 3.5),GenomicRanges, IRanges, S4Vectors,ggplot2,foreach,Rtsne,
21 
+    R(>= 3.4.1),
22 
+    GenomicRanges,
23 
+    IRanges,
24 
+    S4Vectors,
25 
+    ggplot2,
26 
+    foreach,
27 
+    Rtsne,
21 28 
     igraph
22 29 
 License: Artistic-2.0
23 30 
 biocViews:
24 31 
     DNAMethylation, Epigenetics, MethylSeq, Sequencing, Software
25 32 
 Imports:
26 
-    data.table, doParallel, EntropyExplorer, graphics, stats,
27 
-    grDevices, pheatmap, utils, qvalue,
28 
-    WGCNA, ReactomePA
29 
-Maintainer: Xiaowen Chen <Xiaowen.Chen@jax.org>
30 
-Author: Xiaowen Chen [aut, cre], Haitham Ashoor [aut],
31 
-    Ryan Musich [aut], Jiahui Wang [aut], Sheng Li [aut]
33 
+    data.table,
34 
+    doParallel,
35 
+    EntropyExplorer,
36 
+    graphics,
37 
+    stats,
38 
+    grDevices,
39 
+    pheatmap,
40 
+    utils,
41 
+    qvalue,
42 
+    WGCNA,
43 
+    ReactomePA
32 44 
 Encoding: UTF-8
33 
-LazyData: true
34 45 
 RoxygenNote: 6.0.1
35 
-Suggests: knitr,clusterProfiler,ggfortify,org.Hs.eg.db,
46 
+Suggests:
47 
+    knitr,
48 
+    clusterProfiler,
49 
+    ggfortify,
50 
+    org.Hs.eg.db,
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     rmarkdown
37 52 
 VignetteBuilder: knitr
38 53 
 BuildVignettes: TRUE
54 
+URL: https://github.com/TheJacksonLaboratory/epihet
55 
+BugReports: https://github.com/TheJacksonLaboratory/epihet/issues
Browse code

Update DESCRIPTION

xiaowen chen authored on 05/10/2018 21:59:21 • GitHub committed on 05/10/2018 21:59:21
Showing1 changed files
DESCRIPTION
History View file @1ea2099
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 3 
 Date: 2018-04-10
4 
-Version: 0.99.2
4 
+Version: 0.99.3
5 5 
 Authors@R: c(person("Xiaowen", "Chen", email = "Xiaowen.Chen@jax.org",
6 6 
     role = c("aut", "cre")),person("Haitham", "Ashoor",
7 7 
     role = c("aut")),person("Ryan", "Musich", role = c("aut")),
Browse code

rm .gitattributes

Xiaowen Chen authored on 05/10/2018 21:58:19
Showing1 changed files
DESCRIPTION
History View file @220d35f
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 3 
 Date: 2018-04-10
4 
-Version: 0.99.1
4 
+Version: 0.99.2
5 5 
 Authors@R: c(person("Xiaowen", "Chen", email = "Xiaowen.Chen@jax.org",
6 6 
     role = c("aut", "cre")),person("Haitham", "Ashoor",
7 7 
     role = c("aut")),person("Ryan", "Musich", role = c("aut")),
Browse code

remove set.seed and change R dependency R3.5

Xiaowen Chen authored on 05/10/2018 20:08:27
Showing1 changed files
DESCRIPTION
History View file @874a2d2
... ... 
@@ -17,7 +17,7 @@ Description: epihet is an R-package that calculates the epigenetic
17 17 
     created by calculating the differential heterogeneity of the samples.
18 18 
     And we construct co-epihet network and perform network analysis.
19 19 
 Depends:
20 
-    R(>= 3.4),GenomicRanges, IRanges, S4Vectors,ggplot2,foreach,Rtsne,
20 
+    R(>= 3.5),GenomicRanges, IRanges, S4Vectors,ggplot2,foreach,Rtsne,
21 21 
     igraph
22 22 
 License: Artistic-2.0
23 23 
 biocViews:
Browse code

Update DESCRIPTION

xiaowen chen authored on 03/10/2018 17:07:19 • GitHub committed on 03/10/2018 17:07:19
Showing1 changed files
DESCRIPTION
History View file @a27955c
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: epihet
2 2 
 Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 3 
 Date: 2018-04-10
4 
-Version: 0.99.0
4 
+Version: 0.99.1
5 5 
 Authors@R: c(person("Xiaowen", "Chen", email = "Xiaowen.Chen@jax.org",
6 6 
     role = c("aut", "cre")),person("Haitham", "Ashoor",
7 7 
     role = c("aut")),person("Ryan", "Musich", role = c("aut")),
Browse code

remove methclone

Xiaowen Chen authored on 02/10/2018 16:48:44
Showing1 changed files
DESCRIPTION
History View file @1d917d8
... ... 
@@ -4,8 +4,7 @@ Date: 2018-04-10
4 4 
 Version: 0.99.0
5 5 
 Authors@R: c(person("Xiaowen", "Chen", email = "Xiaowen.Chen@jax.org",
6 6 
     role = c("aut", "cre")),person("Haitham", "Ashoor",
7 
-    role = c("aut")),person("Ryan", "Musich",
8 
-    email = "rjmusich@gmail.com",role = c("aut")),
7 
+    role = c("aut")),person("Ryan", "Musich", role = c("aut")),
9 8 
     person("Jiahui","Wang",role = "aut"),person("Sheng", "Li", role = "aut"))
10 9 
 Description: epihet is an R-package that calculates the epigenetic
11 10 
     heterogeneity between cancer cells and/or normal cells. The functions
... ... 
@@ -18,19 +17,18 @@ Description: epihet is an R-package that calculates the epigenetic
18 17 
     created by calculating the differential heterogeneity of the samples.
19 18 
     And we construct co-epihet network and perform network analysis.
20 19 
 Depends:
21 
-    R(>= 3.3),GenomicRanges, IRanges, S4Vectors,ggplot2,foreach,Rtsne,
20 
+    R(>= 3.4),GenomicRanges, IRanges, S4Vectors,ggplot2,foreach,Rtsne,
22 21 
     igraph
23 22 
 License: Artistic-2.0
24 23 
 biocViews:
25 24 
     DNAMethylation, Epigenetics, MethylSeq, Sequencing, Software
26 25 
 Imports:
27 26 
     data.table, doParallel, EntropyExplorer, graphics, stats,
28 
-    grDevices, pheatmap,Rcpp, utils, qvalue,
27 
+    grDevices, pheatmap, utils, qvalue,
29 28 
     WGCNA, ReactomePA
30 
-LinkingTo: Rcpp
31 29 
 Maintainer: Xiaowen Chen <Xiaowen.Chen@jax.org>
32 
-Author: Xiaowen Chen [aut, cre], Haitham Ashoor [aut, cre],
33 
-    Ryan Musich [aut, cre], Jiahui Wang [aut], Sheng Li [aut]
30 
+Author: Xiaowen Chen [aut, cre], Haitham Ashoor [aut],
31 
+    Ryan Musich [aut], Jiahui Wang [aut], Sheng Li [aut]
34 32 
 Encoding: UTF-8
35 33 
 LazyData: true
36 34 
 RoxygenNote: 6.0.1
Browse code

Update DESCRIPTION

xiaowen chen authored on 14/05/2018 15:49:48 • GitHub committed on 14/05/2018 15:49:48
Showing1 changed files
DESCRIPTION
History View file @fa60344
... ... 
@@ -24,7 +24,7 @@ License: Artistic-2.0
24 24 
 biocViews:
25 25 
     DNAMethylation, Epigenetics, MethylSeq, Sequencing, Software
26 26 
 Imports:
27 
-    data.table, doMC, EntropyExplorer, graphics, stats,
27 
+    data.table, doParallel, EntropyExplorer, graphics, stats,
28 28 
     grDevices, pheatmap,Rcpp, utils, qvalue,
29 29 
     WGCNA, ReactomePA
30 30 
 LinkingTo: Rcpp
... ... 
@@ -34,7 +34,7 @@ Author: Xiaowen Chen [aut, cre], Haitham Ashoor [aut, cre],
34 34 
 Encoding: UTF-8
35 35 
 LazyData: true
36 36 
 RoxygenNote: 6.0.1
37 
-Suggests: knitr,clusterProfiler,doParallel,ggfortify,
37 
+Suggests: knitr,clusterProfiler,ggfortify,org.Hs.eg.db,
38 38 
     rmarkdown
39 39 
 VignetteBuilder: knitr
40 40 
 BuildVignettes: TRUE
Browse code

First commit

Haitham Ashoor authored on 23/04/2018 17:08:09
Showing1 changed files
DESCRIPTION
History View file @ef1d8e0
1 1 
new file mode 100755
... ... 
@@ -0,0 +1,40 @@
1 
+Package: epihet
2 
+Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
3 
+Date: 2018-04-10
4 
+Version: 0.99.0
5 
+Authors@R: c(person("Xiaowen", "Chen", email = "Xiaowen.Chen@jax.org",
6 
+    role = c("aut", "cre")),person("Haitham", "Ashoor",
7 
+    role = c("aut")),person("Ryan", "Musich",
8 
+    email = "rjmusich@gmail.com",role = c("aut")),
9 
+    person("Jiahui","Wang",role = "aut"),person("Sheng", "Li", role = "aut"))
10 
+Description: epihet is an R-package that calculates the epigenetic
11 
+    heterogeneity between cancer cells and/or normal cells. The functions
12 
+    establish a pipeline that take in bisulfite sequencing data from multiple
13 
+    samples and use the data to track similarities and differences in
14 
+    epipolymorphism,proportion of discordantly methylated sequencing reads
15 
+    (PDR),and Shannon entropy values at epialleles that are shared between
16 
+    the samples.epihet can be used to perform analysis on the data by creating
17 
+    pheatmaps, box plots, PCA plots, and t-SNE plots. MA plots can also be
18 
+    created by calculating the differential heterogeneity of the samples.
19 
+    And we construct co-epihet network and perform network analysis.
20 
+Depends:
21 
+    R(>= 3.3),GenomicRanges, IRanges, S4Vectors,ggplot2,foreach,Rtsne,
22 
+    igraph
23 
+License: Artistic-2.0
24 
+biocViews:
25 
+    DNAMethylation, Epigenetics, MethylSeq, Sequencing, Software
26 
+Imports:
27 
+    data.table, doMC, EntropyExplorer, graphics, stats,
28 
+    grDevices, pheatmap,Rcpp, utils, qvalue,
29 
+    WGCNA, ReactomePA
30 
+LinkingTo: Rcpp
31 
+Maintainer: Xiaowen Chen <Xiaowen.Chen@jax.org>
32 
+Author: Xiaowen Chen [aut, cre], Haitham Ashoor [aut, cre],
33 
+    Ryan Musich [aut, cre], Jiahui Wang [aut], Sheng Li [aut]
34 
+Encoding: UTF-8
35 
+LazyData: true
36 
+RoxygenNote: 6.0.1
37 
+Suggests: knitr,clusterProfiler,doParallel,ggfortify,
38 
+    rmarkdown
39 
+VignetteBuilder: knitr
40 
+BuildVignettes: TRUE