1. metagenomeSeq
  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 15:08:06
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History View file @ 706cc16
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.40.0
3 
+Version: 1.41.0
4 4 
 Date: 2019-07-12
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia,
6 6 
     Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
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 15:08:06
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.39.0
3 
+Version: 1.40.0
4 4 
 Date: 2019-07-12
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia,
6 6 
     Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
Browse code

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

Nitesh Turaga authored on 26/04/2022 15:14:17
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.38.0
3 
+Version: 1.39.0
4 4 
 Date: 2019-07-12
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia,
6 6 
     Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
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 15:14:17
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.37.0
3 
+Version: 1.38.0
4 4 
 Date: 2019-07-12
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia,
6 6 
     Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
Browse code

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

Nitesh Turaga authored on 26/10/2021 16:07:35
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.36.0
3 
+Version: 1.37.0
4 4 
 Date: 2019-07-12
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia,
6 6 
     Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
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 16:07:35
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.35.0
3 
+Version: 1.36.0
4 4 
 Date: 2019-07-12
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia,
6 6 
     Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
Browse code

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

Nitesh Turaga authored on 19/05/2021 15:58:25
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.34.0
3 
+Version: 1.35.0
4 4 
 Date: 2019-07-12
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia,
6 6 
     Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
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 15:58:25
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@@ -1,6 +1,6 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.33.0
3 
+Version: 1.34.0
4 4 
 Date: 2019-07-12
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia,
6 6 
     Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
Browse code

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

Nitesh Turaga authored on 27/10/2020 14:50:08
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.32.0
3 
+Version: 1.33.0
4 4 
 Date: 2019-07-12
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia,
6 6 
     Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
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 14:50:08
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DESCRIPTION
History View file @ 22ffea0
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.31.0
3 
+Version: 1.32.0
4 4 
 Date: 2019-07-12
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia,
6 6 
     Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
Browse code

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

Nitesh Turaga authored on 27/04/2020 18:34:03
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DESCRIPTION
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@@ -1,6 +1,6 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.30.0
3 
+Version: 1.31.0
4 4 
 Date: 2019-07-12
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia,
6 6 
     Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
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 18:34:03
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DESCRIPTION
History View file @ 7a6db6b
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@@ -1,6 +1,6 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.29.4
3 
+Version: 1.30.0
4 4 
 Date: 2019-07-12
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia,
6 6 
     Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
Browse code

version bump v1.29.4

hcorrada authored on 24/03/2020 19:29:11
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DESCRIPTION
History View file @ 690e3b3
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@@ -1,6 +1,6 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.29.3
3 
+Version: 1.29.4
4 4 
 Date: 2019-07-12
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia,
6 6 
     Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
Browse code

version bump v1.29.3

hcorrada authored on 17/03/2020 17:43:00
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History View file @ d64cfb2
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@@ -1,6 +1,6 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.29.2
3 
+Version: 1.29.3
4 4 
 Date: 2019-07-12
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia,
6 6 
     Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
Browse code

update man pages from Roxygen

hcorrada authored on 17/03/2020 15:54:43
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DESCRIPTION
History View file @ 679f8af
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@@ -47,4 +47,4 @@ BugReports: https://github.com/nosson/metagenomeSeq/issues
47 47 
 biocViews: ImmunoOncology, Classification, Clustering, GeneticVariability,
48 48 
     DifferentialExpression, Microbiome, Metagenomics, Normalization, Visualization,
49 49 
     MultipleComparison, Sequencing, Software
50 
-RoxygenNote: 6.1.1
50 
+RoxygenNote: 7.1.0
Browse code

version bump v1.29.2

hcorrada authored on 03/02/2020 04:14:42
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DESCRIPTION
History View file @ 341833c
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@@ -1,6 +1,6 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.29.1
3 
+Version: 1.29.2
4 4 
 Date: 2019-07-12
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia,
6 6 
     Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
Browse code

version bump v1.29.1

hcorrada authored on 31/10/2019 19:57:21
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History View file @ e9959ed
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@@ -1,6 +1,6 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.29.0
3 
+Version: 1.29.1
4 4 
 Date: 2019-07-12
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia,
6 6 
     Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
Browse code

move ihw to suggests

hcorrada authored on 31/10/2019 18:54:28
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DESCRIPTION
History View file @ a6d51e9
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@@ -28,7 +28,8 @@ Suggests:
28 28 
     gss,
29 29 
     testthat (>= 0.8),
30 30 
     vegan,
31 
-    interactiveDisplay
31 
+    interactiveDisplay,
32 
+    IHW
32 33 
 Imports:
33 34 
     parallel,
34 35 
     matrixStats,
... ... 
@@ -39,8 +40,7 @@ Imports:
39 40 
     grDevices,
40 41 
     stats,
41 42 
     utils,
42 
-    Wrench,
43 
-    IHW
43 
+    Wrench
44 44 
 VignetteBuilder: knitr
45 45 
 URL: https://github.com/nosson/metagenomeSeq/
46 46 
 BugReports: https://github.com/nosson/metagenomeSeq/issues
Browse code

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

Nitesh Turaga authored on 29/10/2019 17:36:48
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@@ -1,6 +1,6 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.28.0
3 
+Version: 1.29.0
4 4 
 Date: 2019-07-12
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia,
6 6 
     Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
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 17:08:38
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DESCRIPTION
History View file @ b241e6e
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@@ -1,6 +1,6 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.27.3
3 
+Version: 1.28.0
4 4 
 Date: 2019-07-12
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia,
6 6 
     Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
Browse code

version bump v1.27.3

hcorrada authored on 04/08/2019 16:55:06
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DESCRIPTION
History View file @ d6068e4
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@@ -1,6 +1,6 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.27.2
3 
+Version: 1.27.3
4 4 
 Date: 2019-07-12
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia,
6 6 
     Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
Browse code

version bump v1.27.2

hcorrada authored on 12/07/2019 17:40:56
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DESCRIPTION
History View file @ af3502a
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@@ -1,7 +1,7 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.27.1
4 
-Date: 2019-07-11
3 
+Version: 1.27.2
4 
+Date: 2019-07-12
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia,
6 6 
     Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
7 7 
 Maintainer: Joseph N. Paulson <jpaulson@jimmy.harvard.edu>
Browse code

version bump v1.27.1

hcorrada authored on 11/07/2019 20:27:02
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DESCRIPTION
History View file @ addc70e
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@@ -1,7 +1,7 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.27.0
4 
-Date: 2016-07-21
3 
+Version: 1.27.1
4 
+Date: 2019-07-11
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia,
6 6 
     Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
7 7 
 Maintainer: Joseph N. Paulson <jpaulson@jimmy.harvard.edu>
Browse code

Updated Authors in DESCRIPTION file

Domenick Braccia authored on 11/07/2019 20:08:14 • hcorrada committed on 11/07/2019 20:24:24
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DESCRIPTION
History View file @ 954307a
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@@ -2,8 +2,8 @@ Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 3 
 Version: 1.27.0
4 4 
 Date: 2016-07-21
5 
-Author: Joseph Nathaniel Paulson, Nathan D. Olson, Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada
6 
-    Bravo
5 
+Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia,
6 
+    Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
7 7 
 Maintainer: Joseph N. Paulson <jpaulson@jimmy.harvard.edu>
8 8 
 Description: metagenomeSeq is designed to determine features (be it
9 9 
     Operational Taxanomic Unit (OTU), species, etc.) that are
Browse code

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

Nitesh Turaga authored on 02/05/2019 16:11:21
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History View file @ b09227a
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@@ -1,6 +1,6 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.26.0
3 
+Version: 1.27.0
4 4 
 Date: 2016-07-21
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
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 15:53:42
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DESCRIPTION
History View file @ 40fa56c
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@@ -1,6 +1,6 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.25.5
3 
+Version: 1.26.0
4 4 
 Date: 2016-07-21
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

version bump v1.25.5

hcorrada authored on 22/04/2019 17:45:11
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History View file @ 16c7c4e
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@@ -1,6 +1,6 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.25.4
3 
+Version: 1.25.5
4 4 
 Date: 2016-07-21
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

made various changes:

updated: DESCRIPTION, NAMESPACE, NEWS, metagenomeSeq vignette,
cumNorm and wrenchNorm code & man pages, and test-fitZig.R

Domenick Braccia authored on 19/04/2019 23:47:21
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DESCRIPTION
History View file @ a360eda
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@@ -39,7 +39,8 @@ Imports:
39 39 
     grDevices,
40 40 
     stats,
41 41 
     utils,
42 
-    Wrench
42 
+    Wrench,
43 
+    IHW
43 44 
 VignetteBuilder: knitr
44 45 
 URL: https://github.com/nosson/metagenomeSeq/
45 46 
 BugReports: https://github.com/nosson/metagenomeSeq/issues
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version bump v1.25.4

hcorrada authored on 10/04/2019 18:01:06
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DESCRIPTION
History View file @ 867f3df
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@@ -1,6 +1,6 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.25.3
3 
+Version: 1.25.4
4 4 
 Date: 2016-07-21
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

version bump v1.25.3

hcorrada authored on 27/02/2019 15:35:57
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DESCRIPTION
History View file @ 237560f
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@@ -1,6 +1,6 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.25.2
3 
+Version: 1.25.3
4 4 
 Date: 2016-07-21
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

version bump v1.25.2

hcorrada authored on 25/02/2019 21:46:12
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DESCRIPTION
History View file @ 053dc20
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@@ -1,6 +1,6 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.25.1
3 
+Version: 1.25.2
4 4 
 Date: 2016-07-21
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

Merge branch 'master' of https://github.com/HCBravoLab/metagenomeSeq

hcorrada authored on 25/02/2019 21:45:21
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Updated .rda files and test files

.rda files for lungData and mouseData are now stored with the expSummary slot
being of class "list" instead of "environment".

Domenick Braccia authored on 05/02/2019 18:41:26
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DESCRIPTION
History View file @ d113d81
... ... 
@@ -19,7 +19,7 @@ Depends:
19 19 
     limma,
20 20 
     glmnet,
21 21 
     methods,
22 
-    RColorBrewer
22 
+    RColorBrewer
23 23 
 Suggests:
24 24 
     annotate,
25 25 
     BiocGenerics,
... ... 
@@ -34,7 +34,12 @@ Imports:
34 34 
     matrixStats,
35 35 
     foreach,
36 36 
     Matrix,
37 
-    gplots
37 
+    gplots,
38 
+    graphics,
39 
+    grDevices,
40 
+    stats,
41 
+    utils,
42 
+    Wrench
38 43 
 VignetteBuilder: knitr
39 44 
 URL: https://github.com/nosson/metagenomeSeq/
40 45 
 BugReports: https://github.com/nosson/metagenomeSeq/issues
Browse code

Updating DESCRIPTION, NAMESPACE and R/allClasses.R

Domenick Braccia authored on 04/02/2019 22:15:43
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DESCRIPTION
History View file @ 65d6c5b
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@@ -41,4 +41,4 @@ BugReports: https://github.com/nosson/metagenomeSeq/issues
41 41 
 biocViews: Classification, Clustering, GeneticVariability,
42 42 
     DifferentialExpression, Microbiome, Metagenomics, Normalization, Visualization,
43 43 
     MultipleComparison, Sequencing, Software
44 
-RoxygenNote: 6.0.1
44 
+RoxygenNote: 6.1.1
Browse code

Add ImmunoOncology biocViews term

Kayla-Morrell authored on 04/01/2019 18:10:42
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DESCRIPTION
History View file @ 80319dd
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@@ -1,6 +1,6 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.25.0
3 
+Version: 1.25.1
4 4 
 Date: 2016-07-21
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
... ... 
@@ -38,7 +38,7 @@ Imports:
38 38 
 VignetteBuilder: knitr
39 39 
 URL: https://github.com/nosson/metagenomeSeq/
40 40 
 BugReports: https://github.com/nosson/metagenomeSeq/issues
41 
-biocViews: Classification, Clustering, GeneticVariability,
41 
+biocViews: ImmunoOncology, Classification, Clustering, GeneticVariability,
42 42 
     DifferentialExpression, Microbiome, Metagenomics, Normalization, Visualization,
43 43 
     MultipleComparison, Sequencing, Software
44 44 
 RoxygenNote: 6.0.1
Browse code

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

vobencha authored on 30/10/2018 15:54:31
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DESCRIPTION
History View file @ 5f33b40
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@@ -1,6 +1,6 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.24.0
3 
+Version: 1.25.0
4 4 
 Date: 2016-07-21
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

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

vobencha authored on 30/10/2018 15:41:51
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DESCRIPTION
History View file @ c584c06
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@@ -1,6 +1,6 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.23.1
3 
+Version: 1.24.0
4 4 
 Date: 2016-07-21
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

replace BiocInstaller biocLite mentions with BiocManager

LiNk-NY authored on 30/08/2018 17:51:56
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DESCRIPTION
History View file @ 40d4c39
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@@ -1,6 +1,6 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.23.0
3 
+Version: 1.23.1
4 4 
 Date: 2016-07-21
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

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

vobencha authored on 30/04/2018 14:41:39
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 Package: metagenomeSeq
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 Date: 2016-07-21
5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
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bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:35:29
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5 5 
 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
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version bump v1.21.2

hcorrada authored on 11/04/2018 09:07:51
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 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
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version bump v1.21.1

hcorrada authored on 11/12/2017 19:12:24
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 Author: Joseph Nathaniel Paulson, Nathan D. Olson, Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
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update author list

hcorrada authored on 11/12/2017 19:07:23
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-Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
5 
+Author: Joseph Nathaniel Paulson, Nathan D. Olson, Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
7 7 
 Maintainer: Joseph N. Paulson <jpaulson@jimmy.harvard.edu>
8 8 
 Description: metagenomeSeq is designed to determine features (be it
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bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:52:47
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6 6 
     Bravo
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bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:40:01
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5 5 
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6 6 
     Bravo
Browse code

bump x.y.z versions to odd y after creation of 3_5 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@129129 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:50:57
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5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

bump x.y.z versions to even y prior to creation of 3_5 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@129126 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:25:24
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5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

remove print statement; version bump

From: hcorrada <hcorrada@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@128747 bc3139a8-67e5-0310-9ffc-ced21a209358

Hector Corrada Bravo authored on 15/04/2017 21:50:57
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5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

version bump

From: hcorrada <hcorrada@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@128607 bc3139a8-67e5-0310-9ffc-ced21a209358

Hector Corrada Bravo authored on 12/04/2017 16:21:16
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5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

version bump

From: hcorrada <hcorrada@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@128148 bc3139a8-67e5-0310-9ffc-ced21a209358

Hector Corrada Bravo authored on 06/04/2017 17:27:34
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5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

update documentation

From: hcorrada <hcorrada@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@128147 bc3139a8-67e5-0310-9ffc-ced21a209358

Hector Corrada Bravo authored on 06/04/2017 17:27:27
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@@ -41,4 +41,4 @@ BugReports: https://github.com/nosson/metagenomeSeq/issues
41 41 
 biocViews: Classification, Clustering, GeneticVariability,
42 42 
     DifferentialExpression, Microbiome, Metagenomics, Normalization, Visualization,
43 43 
     MultipleComparison, Sequencing, Software
44 
-RoxygenNote: 5.0.1
44 
+RoxygenNote: 6.0.1
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bump x.y.z versions to odd 'y' after creation of 3_4 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@122712 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 19:10:43
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4 4 
 Date: 2016-07-21
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

bump x.y.z versions to even 'y' prior to creation of 3_4 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@122710 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 18:45:06
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5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

version bump

From: hcorrada <hcorrada@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@122456 bc3139a8-67e5-0310-9ffc-ced21a209358

Hector Corrada Bravo authored on 15/10/2016 08:30:58
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 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

Wrapper functions to visualize fitTimeSeries results

* update documents
* adding namespace
* add .git to .Rbuildignore
* version bump

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@122430 bc3139a8-67e5-0310-9ffc-ced21a209358

Hector Corrada Bravo authored on 14/10/2016 13:08:56
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5 5 
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6 6 
     Bravo
Browse code

version bump

From: hcorrada <hcorrada@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@121987 bc3139a8-67e5-0310-9ffc-ced21a209358

Hector Corrada Bravo authored on 06/10/2016 18:58:14
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5 5 
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6 6 
     Bravo
Browse code

version bump

From: Hector Corrada Bravo <hcorrada@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@121112 bc3139a8-67e5-0310-9ffc-ced21a209358

Hector Corrada Bravo authored on 19/09/2016 03:10:08
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5 5 
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6 6 
     Bravo
Browse code

updating unit testing package to testthat

From: nosson <jpaulson@umiacs.umd.edu>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@121102 bc3139a8-67e5-0310-9ffc-ced21a209358

Hector Corrada Bravo authored on 19/09/2016 03:09:13
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26 26 
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     knitr,
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     gss,
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30 30 
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     interactiveDisplay
32 32 
 Imports:
Browse code

updating perm pval for fitTimeSeries from #>B to #+1/B+1

From: jnpaulson <nosson@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@119525 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 21/07/2016 13:54:44
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 Package: metagenomeSeq
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 Title: Statistical analysis for sparse high-throughput sequencing
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-Version: 1.15.2
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-Date: 2016-04-17
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+Version: 1.15.3
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+Date: 2016-07-21
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
7 7 
 Maintainer: Joseph N. Paulson <jpaulson@jimmy.harvard.edu>
Browse code

Version bump to trigger package rebuilding now that purl()'ing issue has been correctly identified. knitr does not create purl()'ed (Stangle equivalent) .R files if _R_CHECK_TIMINGS_ is set, which the build system was setting. Now it's not set, so these .R files are now created. See https://github.com/yihui/knitr/issues/1212 for more.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@117512 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 15/05/2016 20:14:22
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5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

Bump version of all packages that use knitr for vignettes. This is because of an issue (now fixed) in knitr which failed to create purl()'ed R files from vignette sources and include them in the package. This version bump will cause these packages to propagate with those R files included.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@117323 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 11/05/2016 23:05:31
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6 6 
     Bravo
Browse code

bump version after creating 3.3 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@117081 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/05/2016 21:30:44
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5 5 
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6 6 
     Bravo
Browse code

Bump versions prior to creation of 3.3 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@117079 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/05/2016 21:20:18
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5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

updated calculation of s2 in calcZeroComponent

From: jnpaulson <nosson@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@116424 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 17/04/2016 20:15:33
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5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

updated man pages

From: jnpaulson <nosson@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@116423 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 17/04/2016 20:15:24
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.13.05
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-Date: 2016-02-26
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+Version: 1.13.06
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+Date: 2016-04-17
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
7 7 
 Maintainer: Joseph N. Paulson <jpaulson@jimmy.harvard.edu>
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38 38 
 VignetteBuilder: knitr
39 39 
 URL: https://github.com/nosson/metagenomeSeq/
40 40 
 BugReports: https://github.com/nosson/metagenomeSeq/issues
41 
-biocViews: Classification, Clustering, GeneticVariability, DifferentialExpression, Microbiome, Metagenomics, Normalization, Visualization, MultipleComparison, Sequencing, Software
41 
+biocViews: Classification, Clustering, GeneticVariability,
42 
+    DifferentialExpression, Microbiome, Metagenomics, Normalization, Visualization,
43 
+    MultipleComparison, Sequencing, Software
44 
+RoxygenNote: 5.0.1
Browse code

Issue #30

From: jnpaulson <nosson@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@114078 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 28/02/2016 16:59:50
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1 1 
 Package: metagenomeSeq
2 2 
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-Version: 1.13.04
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+Version: 1.13.05
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 Date: 2016-02-26
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

Issue 32 from https://github.com/HCBravoLab/metagenomeSeq/issues/32

From: jnpaulson <nosson@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@114077 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 28/02/2016 16:59:33
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
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-Version: 1.13.03
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-Date: 2016-02-18
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+Version: 1.13.04
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+Date: 2016-02-26
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
7 
-Maintainer: Joseph N. Paulson <jpaulson@umiacs.umd.edu>
7 
+Maintainer: Joseph N. Paulson <jpaulson@jimmy.harvard.edu>
8 8 
 Description: metagenomeSeq is designed to determine features (be it
9 9 
     Operational Taxanomic Unit (OTU), species, etc.) that are
10 10 
     differentially abundant between two or more groups of multiple
Browse code

changing unique to levels call in fitPA

From: nosson <jpaulson@umiacs.umd.edu>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@113757 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 18/02/2016 16:52:55
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.13.02
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-Date: 2015-12-14
3 
+Version: 1.13.03
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+Date: 2016-02-18
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
7 7 
 Maintainer: Joseph N. Paulson <jpaulson@umiacs.umd.edu>
Browse code

closing https://github.com/HCBravoLab/metagenomeSeq/issues/7

From: jnpaulson <nosson@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@111515 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 15/12/2015 19:24:23
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.13.01
3 
+Version: 1.13.02
4 4 
 Date: 2015-12-14
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

upgrading from biom to biomformat for biom-format vs 2.0 support

From: nosson <jpaulson@umiacs.umd.edu>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@111486 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 15/12/2015 05:11:47
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@@ -1,7 +1,7 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.13.0
4 
-Date: 2015-09-17
3 
+Version: 1.13.01
4 
+Date: 2015-12-14
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
7 7 
 Maintainer: Joseph N. Paulson <jpaulson@umiacs.umd.edu>
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@@ -23,7 +23,7 @@ Depends:
23 23 
 Suggests:
24 24 
     annotate,
25 25 
     BiocGenerics,
26 
-    biom,
26 
+    biomformat,
27 27 
     knitr,
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     gss,
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     RUnit,
Browse code

Bumped version number of all packages after creation of 3.2 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@109592 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2015 19:59:53
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.12.0
3 
+Version: 1.13.0
4 4 
 Date: 2015-09-17
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

Bumped versions of all packages prior to creating 3.2 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@109589 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2015 19:36:05
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.11.16
3 
+Version: 1.12.0
4 4 
 Date: 2015-09-17
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

Upgrading w/o git svn bridge

From: jnpaulson <nosson@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@109105 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 02/10/2015 14:15:35
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.11.10
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-Date: 2015-05-26
3 
+Version: 1.11.16
4 
+Date: 2015-09-17
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
7 7 
 Maintainer: Joseph N. Paulson <jpaulson@umiacs.umd.edu>
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 6dfc3da592d22f17356b7b91c9e646b35b467ae3

fixing latex compilation issues



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@104218 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 26/05/2015 18:47:36
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.11.09
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-Date: 2015-05-15
3 
+Version: 1.11.10
4 
+Date: 2015-05-26
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
7 7 
 Maintainer: Joseph N. Paulson <jpaulson@umiacs.umd.edu>
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: f54298b23a84fcde2209ed7d874fe89e1aff6576

fixing vignette



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@104039 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 21/05/2015 14:51:51
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.11.08
3 
+Version: 1.11.09
4 4 
 Date: 2015-05-15
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: a1b195cd9621682fb94068feb439e6d32e171b1b

addded mention in vignette



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@103925 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 18/05/2015 15:47:27
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.11.07
4 
-Date: 2015-05-12
3 
+Version: 1.11.08
4 
+Date: 2015-05-15
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
7 7 
 Maintainer: Joseph N. Paulson <jpaulson@umiacs.umd.edu>
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: e8c7750ff220036cb51ace6dc52af1ecc7dc3d47

speeding up examples



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@103678 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 12/05/2015 05:48:11
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@@ -1,6 +1,6 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.11.05
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+Version: 1.11.07
4 4 
 Date: 2015-05-12
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
... ... 
@@ -19,7 +19,6 @@ Depends:
19 19 
     limma,
20 20 
     glmnet,
21 21 
     methods,
22 
-    glmnet,
23 22 
     RColorBrewer
24 23 
 Suggests:
25 24 
     annotate,
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: f228152638ce533024128de813d8b2855f26f34b

modifying MRfulltable/table/coefs to accept fitFeatureModel as well



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@103677 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 12/05/2015 05:28:19
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.11.03
3 
+Version: 1.11.05
4 4 
 Date: 2015-05-12
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 6fdda27eb65d0b343c088440274c6831d846eb32

software fix



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@103674 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 12/05/2015 04:17:08
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.11.02
4 
-Date: 2015-05-11
3 
+Version: 1.11.03
4 
+Date: 2015-05-12
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
7 7 
 Maintainer: Joseph N. Paulson <jpaulson@umiacs.umd.edu>
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 3dfc168525aed75b27c1bca161eff4f207554e0d

uptick



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@103668 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 12/05/2015 00:11:43
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@@ -1,6 +1,6 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.11.01
3 
+Version: 1.11.02
4 4 
 Date: 2015-05-11
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: c7faf0526a00f718e1fd9285d76f2216852ad115

Merge branch 'wgs'


Commit id: dd46fdfd9565c673f0a5ae2a885bd3050b31586f

adding required namespace, description, etc


Commit id: 3a1d5b7a1d44c18bd9962b223030964927660d8b

Merge branch 'wgs' of https://github.com/nosson/metagenomeSeq into wgs


Commit id: bf5591aaa1af549293fd17a14f31a7602d78585c

Adding fitFeatureModel to wgs branch


Commit id: fb291bfd25b2301ea0be95a2b16d87bed922a21b

adding citation


Commit id: 2575df5ef4e5deaa4b373e222f03be2f6b1da8c7

Updating requirements in DESCRIPTION


Commit id: 9261688c0f34b0ee86ffc4daaccee0feb327bee0

Adding fitFeatureModel to wgs branch


Commit id: efab9f028c91f4ba32b73992160cf6530fa67f02

modify zero M-step


Commit id: 6a38ca85a2e9a1605afc1bf781ab00e35ebdb082

keeping zeroLM



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@103667 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 12/05/2015 00:07:46
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@@ -1,7 +1,7 @@
1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.11.0
4 
-Date: 2015-04-01
3 
+Version: 1.11.01
4 
+Date: 2015-05-11
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
7 7 
 Maintainer: Joseph N. Paulson <jpaulson@umiacs.umd.edu>
... ... 
@@ -17,7 +17,9 @@ Depends:
17 17 
     R(>= 3.0),
18 18 
     Biobase,
19 19 
     limma,
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+    glmnet,
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     methods,
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+    glmnet,
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     RColorBrewer
22 24 
 Suggests:
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     annotate,
... ... 
@@ -31,6 +33,8 @@ Suggests:
31 33 
 Imports:
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     parallel,
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     matrixStats,
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+    foreach,
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+    Matrix,
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     gplots
35 39 
 VignetteBuilder: knitr
36 40 
 URL: https://github.com/nosson/metagenomeSeq/
Browse code

Bump versions in trunk after creation of 3.1 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@102594 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 16/04/2015 20:02:44
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.10.0
3 
+Version: 1.11.0
4 4 
 Date: 2015-04-01
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

Bump versions prior to creating 3.1 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@102591 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 16/04/2015 19:42:01
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.9.32
3 
+Version: 1.10.0
4 4 
 Date: 2015-04-01
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: ecfca4d5b491c1bec2a57bd81c9ed7ccfe193970

renaming fitMeta -> fitLogNormal (more appropriately named)



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@101722 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 01/04/2015 17:15:11
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.9.31
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-Date: 2015-3-11
3 
+Version: 1.9.32
4 
+Date: 2015-04-01
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
7 7 
 Maintainer: Joseph N. Paulson <jpaulson@umiacs.umd.edu>
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: aa5e246702c60b5de8a4b203bb4652d0260371e7

adding fixes due to updates for mouseData taxonomy



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@100580 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 12/03/2015 02:37:31
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.9.30
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+Version: 1.9.31
4 4 
 Date: 2015-3-11
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: d2ab43afc28741e4da5b868a82bb26162bd55ced

many minor tweaks



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@100579 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 12/03/2015 02:20:42
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.9.29
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-Date: 2015-2-10
3 
+Version: 1.9.30
4 
+Date: 2015-3-11
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
7 7 
 Maintainer: Joseph N. Paulson <jpaulson@umiacs.umd.edu>
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit.

Commit information:

Commit id: 40232238d23094c287d4755786f41546d94bad6d

fixing example error

Committed by: nosson
Author Name: nosson
Commit date: 2015-02-19 16:51:52 -0500
Author date: 2015-02-19 16:51:52 -0500


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@99625 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 19/02/2015 21:52:03
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
3 
-Version: 1.9.28
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+Version: 1.9.29
4 4 
 Date: 2015-2-10
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
6 6 
     Bravo
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit.

Commit information:

Commit id: 56ae4c617b9ef28fa5adad5e85c1eedfb1f54113

fixing https://support.bioconductor.org/p/65068/

Committed by: nosson
Author Name: nosson
Commit date: 2015-02-18 16:58:13 -0500
Author date: 2015-02-18 16:58:13 -0500


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@99596 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 18/02/2015 21:58:21
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1 1 
 Package: metagenomeSeq
2 2 
 Title: Statistical analysis for sparse high-throughput sequencing
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-Version: 1.9.27
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+Version: 1.9.28
4 4 
 Date: 2015-2-10
5 5 
 Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
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