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Jeanette Johnson authored on 21/03/2023 21:44:23 • jeanettejohnson committed on 21/03/2023 23:14:59
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README.md

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@@ -10,21 +10,20 @@ Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC ma
                                      # Installing CoGAPS
                                     -*CoGAPS* is a bioconductor R package ([link](https://bioconductor.org/packages/CoGAPS)) and so the release version can be installed
                                     -as follows:
                                     +Via Bioconductor:
                                      ```
                                      install.packages("BiocManager")
                                     -BiocManager::install("CoGAPS")
                                     +BiocManager::install("FertigLab/CoGAPS")
                                      ```
                                      The most up-to-date version of *CoGAPS* can be installed directly from the
                                      *FertigLab* Github Repository:
                                      ```
                                     -BiocManager::install("FertigLab/CoGAPS")
                                     +devtools::install_github("FertigLab/CoGAPS")
                                      ```
                                      # Using CoGAPS
                                     -Follow the vignette [here](https://www.bioconductor.org/packages/devel/bioc/vignettes/CoGAPS/inst/doc/CoGAPS.html)
                                     +Follow the vignette [here](https://github.com/FertigLab/CoGAPS/blob/master/vignettes/CoGAPS.Rmd)

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Update README.md

Jeanette Johnson authored on 20/05/2022 15:56:33 • jeanettejohnson committed on 18/03/2023 19:33:08
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README.md

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                                      <img src="https://user-images.githubusercontent.com/25310425/169565420-56958b50-29a2-4032-afb3-08447577d074.png" width="300">
+                                    +
                                      # CoGAPS (Version: 3.11.1)
+                                    +
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)
                                      [![Build Status](https://travis-ci.org/FertigLab/CoGAPS.svg?branch=master)](https://travis-ci.org/FertigLab/CoGAPS)

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Update README.md

Jeanette Johnson authored on 20/05/2022 15:56:15 • jeanettejohnson committed on 18/03/2023 19:33:08
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README.md

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                                     +<img src="https://user-images.githubusercontent.com/25310425/169565420-56958b50-29a2-4032-afb3-08447577d074.png" width="300">
                                      # CoGAPS (Version: 3.11.1)
+                                    -
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)
                                      [![Build Status](https://travis-ci.org/FertigLab/CoGAPS.svg?branch=master)](https://travis-ci.org/FertigLab/CoGAPS)

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Updated version on README

lothm2014 authored on 23/11/2020 12:43:57
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README.md

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                                     -# CoGAPS (Version: 3.9.2)
                                     +# CoGAPS (Version: 3.11.1)
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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Merge branch 'upstream/master' into develop

lothm2014 authored on 16/10/2020 15:36:18
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Updated version in README

Melanie Loth authored on 15/10/2020 19:16:54 • GitHub committed on 15/10/2020 19:16:54
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README.md

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                                     -# CoGAPS (Version: 3.7.0)
                                     +# CoGAPS (Version: 3.9.2)
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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sherman5 authored on 10/08/2020 01:13:21
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                                     -# CoGAPS (Version: 3.7.0)
                                     +# CoGAPS (Version: 3.9.1)
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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Fix some bugs in the documentation

sherman5 authored on 30/06/2020 05:53:52
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README.md

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                                     -# CoGAPS Version: 3.5.13
                                     +# CoGAPS (Version: 3.7.0)
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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version bump 3.5.13

Tom Sherman authored on 10/09/2019 01:24:27
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README.md

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                                     -# CoGAPS Version: 3.5.12
                                     +# CoGAPS Version: 3.5.13
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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Version bump 3.5.12

Tom Sherman authored on 30/08/2019 18:22:36
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                                     -# CoGAPS Version: 3.5.11
                                     +# CoGAPS Version: 3.5.12
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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Version bump 3.5.11

Tom Sherman authored on 30/08/2019 17:42:06
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README.md

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                                     -# CoGAPS Version: 3.5.10
                                     +# CoGAPS Version: 3.5.11
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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Version bump 3.5.10

Tom Sherman authored on 30/08/2019 17:35:53
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README.md

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                                     -# CoGAPS Version: 3.5.9
                                     +# CoGAPS Version: 3.5.10
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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Version bump 3.5.9

sherman5 authored on 29/08/2019 23:37:50
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README.md

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                                     -# CoGAPS Version: 3.5.8
                                     +# CoGAPS Version: 3.5.9
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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Tom Sherman authored on 22/07/2019 21:39:52
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                                     -# CoGAPS Version: 3.5.7
                                     +# CoGAPS Version: 3.5.8
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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Tom Sherman authored on 22/07/2019 20:52:45
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                                     -# CoGAPS Version: 3.5.6
                                     +# CoGAPS Version: 3.5.7
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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version bumP

Tom Sherman authored on 02/07/2019 17:23:21
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                                     -# CoGAPS Version: 3.5.5
                                     +# CoGAPS Version: 3.5.6
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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Tom Sherman authored on 02/07/2019 17:17:17
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                                     -# CoGAPS Version: 3.5.4
                                     +# CoGAPS Version: 3.5.5
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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Tom Sherman authored on 28/06/2019 17:13:46
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README.md

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                                     -# CoGAPS Version: 3.5.3
                                     +# CoGAPS Version: 3.5.4
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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version bump

sherman5 authored on 26/06/2019 19:16:24
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                                     -# CoGAPS
                                     +# CoGAPS Version: 3.5.3
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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version bump

sherman5 authored on 26/06/2019 18:38:48
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                                     -# CoGAPS Version: 3.5.1
                                     +# CoGAPS
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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version bump for new bioc release

Tom Sherman authored on 04/06/2019 16:24:22
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Tom Sherman authored on 04/06/2019 15:18:27
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                                     -# CoGAPS Version: 3.3.44
                                     +# CoGAPS Version: 3.3.45
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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Merge branch 'master' of github.com:FertigLab/CoGAPS

Tom Sherman authored on 01/05/2019 20:21:41
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Tom Sherman authored on 01/05/2019 20:21:05
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README.md

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                                     -# CoGAPS Version: 3.3.43
                                     +# CoGAPS Version: 3.3.44
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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Update README.md

Tom Sherman authored on 30/04/2019 17:10:36 • GitHub committed on 30/04/2019 17:10:36
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README.md

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@@ -8,7 +8,7 @@ Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC ma
                                      # Installing CoGAPS
                                     -*CoGAPS* is a bioconductor R package and so the release version can be installed
                                     +*CoGAPS* is a bioconductor R package ([link](https://bioconductor.org/packages/CoGAPS)) and so the release version can be installed
                                      as follows:
                                      ```

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Update README.md

Tom Sherman authored on 30/04/2019 17:06:44 • GitHub committed on 30/04/2019 17:06:44
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README.md

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@@ -20,11 +20,7 @@ The most up-to-date version of *CoGAPS* can be installed directly from the
                                      *FertigLab* Github Repository:
                                      ```
                                     -## Method 1 using BiocManager
                                      BiocManager::install("FertigLab/CoGAPS")
+                                    -
                                     -## Method 2 using devtools package
                                     -devtools::install_github("FertigLab/CoGAPS")
                                      ```
                                      # Using CoGAPS

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Tom Sherman authored on 03/04/2019 22:03:40
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README.md

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                                     -# CoGAPS Version: 3.3.42
                                     +# CoGAPS Version: 3.3.43
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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Update README.md

Tom Sherman authored on 11/03/2019 15:53:55 • GitHub committed on 11/03/2019 15:53:55
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README.md

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@@ -29,4 +29,4 @@ devtools::install_github("FertigLab/CoGAPS")
                                      # Using CoGAPS
                                     -Follow the vignette [here](http://htmlpreview.github.io/?https://github.com/FertigLab/CoGAPS/blob/develop/vignettes/CoGAPS.html)
                                     +Follow the vignette [here](https://www.bioconductor.org/packages/devel/bioc/vignettes/CoGAPS/inst/doc/CoGAPS.html)

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Update README.md

Tom Sherman authored on 11/03/2019 15:53:18 • GitHub committed on 11/03/2019 15:53:18
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README.md

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@@ -29,4 +29,4 @@ devtools::install_github("FertigLab/CoGAPS")
                                      # Using CoGAPS
                                     -Follow the vignette here: http://htmlpreview.github.io/?https://github.com/FertigLab/CoGAPS/blob/develop/vignettes/CoGAPS.html
                                     +Follow the vignette [here](http://htmlpreview.github.io/?https://github.com/FertigLab/CoGAPS/blob/develop/vignettes/CoGAPS.html)

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version bump

Tom Sherman authored on 08/03/2019 01:50:44
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README.md

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                                     -# CoGAPS Version: 3.3.41
                                     +# CoGAPS Version: 3.3.42
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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Tom Sherman authored on 05/03/2019 23:25:25
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README.md

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                                     -# CoGAPS Version: 3.3.40
                                     +# CoGAPS Version: 3.3.41
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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Tom Sherman authored on 22/02/2019 16:39:40
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README.md

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                                     -# CoGAPS Version: 3.3.39
                                     +# CoGAPS Version: 3.3.40
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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Tom Sherman authored on 20/02/2019 11:37:23
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README.md

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                                     -# CoGAPS Version: 3.3.38
                                     +# CoGAPS Version: 3.3.39
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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version bump

Tom Sherman authored on 19/02/2019 04:17:49
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README.md

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                                     -# CoGAPS Version: 3.3.37
                                     +# CoGAPS Version: 3.3.38
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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Tom Sherman authored on 18/02/2019 19:58:26
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                                     -# CoGAPS Version: 3.3.36
                                     +# CoGAPS Version: 3.3.37
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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updated installation instructions in readme

Tom Sherman authored on 18/02/2019 19:36:28
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README.md

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@@ -12,33 +12,21 @@ Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC ma
                                      as follows:
                                      ```
                                     -source("https://bioconductor.org/biocLite.R")
                                     -biocLite("CoGAPS")
                                     +install.packages("BiocManager")
                                     +BiocManager::install("CoGAPS")
                                      ```
                                      The most up-to-date version of *CoGAPS* can be installed directly from the
                                      *FertigLab* Github Repository:
                                      ```
                                     -## Method 1 using biocLite
                                     -biocLite("FertigLab/CoGAPS", dependencies = TRUE, build_vignettes = TRUE)
                                     +## Method 1 using BiocManager
                                     +BiocManager::install("FertigLab/CoGAPS")
                                      ## Method 2 using devtools package
                                      devtools::install_github("FertigLab/CoGAPS")
                                      ```
                                     -There is also an option to install the development version of *CoGAPS*,
                                     -while this version has the latest experimental features, it is not guaranteed
                                     -to be stable.
+                                    -
                                     -```
                                     -## Method 1 using biocLite
                                     -biocLite("FertigLab/CoGAPS", ref="develop", dependencies = TRUE, build_vignettes = TRUE)
+                                    -
                                     -## Method 2 using devtools package
                                     -devtools::install_github("FertigLab/CoGAPS", ref="develop")
                                     -```
+                                    -
                                      # Using CoGAPS
                                      Follow the vignette here: http://htmlpreview.github.io/?https://github.com/FertigLab/CoGAPS/blob/develop/vignettes/CoGAPS.html

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version bump

Tom Sherman authored on 13/02/2019 20:13:09
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                                     -# CoGAPS Version: 3.3.35
                                     +# CoGAPS Version: 3.3.36
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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Tom Sherman authored on 12/02/2019 20:31:32
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                                     -# CoGAPS Version: 3.3.34
                                     +# CoGAPS Version: 3.3.35
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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Tom Sherman authored on 08/02/2019 20:17:29
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                                     -# CoGAPS Version: 3.3.33
                                     +# CoGAPS Version: 3.3.34
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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fix downloads link

Tom Sherman authored on 07/02/2019 22:02:02 • GitHub committed on 07/02/2019 22:02:02
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README.md

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@@ -1,7 +1,7 @@
                                      # CoGAPS Version: 3.3.33
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                     -[![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)
                                     +[![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)
                                      [![Build Status](https://travis-ci.org/FertigLab/CoGAPS.svg?branch=master)](https://travis-ci.org/FertigLab/CoGAPS)
                                      Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.

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add link to travis in status button

Tom Sherman authored on 07/02/2019 21:58:23 • GitHub committed on 07/02/2019 21:58:23
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README.md

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@@ -2,7 +2,7 @@
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)
                                     -[![Build Status](https://travis-ci.org/FertigLab/CoGAPS.svg?branch=master)](https://travis-ci.org/FertigLab/CoGAPS.svg?branch=master)
                                     +[![Build Status](https://travis-ci.org/FertigLab/CoGAPS.svg?branch=master)](https://travis-ci.org/FertigLab/CoGAPS)
                                      Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.

Browse code

fix embedded travis status

Tom Sherman authored on 07/02/2019 21:57:36 • GitHub committed on 07/02/2019 21:57:36
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README.md

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@@ -2,7 +2,7 @@
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)
                                     -[![Build Status](https://travis-ci.org/FertigLab/CoGAPS.png)](https://travis-ci.org/FertigLab/CoGAPS)
                                     +[![Build Status](https://travis-ci.org/FertigLab/CoGAPS.svg?branch=master)](https://travis-ci.org/FertigLab/CoGAPS.svg?branch=master)
                                      Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.

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embed travis status in readme

Tom Sherman authored on 07/02/2019 21:55:04 • GitHub committed on 07/02/2019 21:55:04
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README.md

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@@ -2,6 +2,7 @@
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)
                                     +[![Build Status](https://travis-ci.org/FertigLab/CoGAPS.png)](https://travis-ci.org/FertigLab/CoGAPS)
                                      Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.
@@ -40,4 +41,4 @@ devtools::install_github("FertigLab/CoGAPS", ref="develop")
                                      # Using CoGAPS
                                     -Follow the vignette here: http://htmlpreview.github.io/?https://github.com/FertigLab/CoGAPS/blob/develop/vignettes/CoGAPS.html
                                     \ No newline at end of file
                                     +Follow the vignette here: http://htmlpreview.github.io/?https://github.com/FertigLab/CoGAPS/blob/develop/vignettes/CoGAPS.html

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bump version

Tom Sherman authored on 07/02/2019 21:48:59
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README.md

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                                     -# CoGAPS Version: 3.3.32
                                     +# CoGAPS Version: 3.3.33
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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version bump

Tom Sherman authored on 04/02/2019 23:03:18
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README.md

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                                     -# CoGAPS Version: 3.3.31
                                     +# CoGAPS Version: 3.3.32
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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version bump

Tom Sherman authored on 31/01/2019 21:42:58
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README.md

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                                     -# CoGAPS Version: 3.3.30
                                     +# CoGAPS Version: 3.3.31
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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added check for params@distributed

Tom Sherman authored on 29/01/2019 20:09:05
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README.md

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                                     -# CoGAPS Version: 3.3.29
                                     +# CoGAPS Version: 3.3.30
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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version bump

Tom Sherman authored on 22/01/2019 23:43:07
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README.md

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                                     -# CoGAPS Version: 3.3.28
                                     +# CoGAPS Version: 3.3.29
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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bumped version

Tom Sherman authored on 15/01/2019 21:56:51
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README.md

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                                     -# CoGAPS Version: 3.3.27
                                     +# CoGAPS Version: 3.3.28
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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stop running long examples

Tom Sherman authored on 09/01/2019 18:29:52
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README.md

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                                     -# CoGAPS Version: 3.3.26
                                     +# CoGAPS Version: 3.3.27
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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updated version

Tom Sherman authored on 08/01/2019 15:42:19
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README.md

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                                     -# CoGAPS Version: 3.3.25
                                     +# CoGAPS Version: 3.3.26
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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updated version

Tom Sherman authored on 07/01/2019 22:09:40
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README.md

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                                     -# CoGAPS Version: 3.3.24
                                     +# CoGAPS Version: 3.3.25
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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speed up compilation by turning off C++ tests by default

Tom Sherman authored on 04/01/2019 21:16:06
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README.md

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                                     -# CoGAPS Version: 3.3.23
                                     +# CoGAPS Version: 3.3.24
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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better handle setting nPatterns after cut

Tom Sherman authored on 04/01/2019 20:12:56
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README.md

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                                     -# CoGAPS Version: 3.3.22
                                     +# CoGAPS Version: 3.3.23
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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fixed bug when reading csv/tsv files with sparseOptimization

Tom Sherman authored on 03/01/2019 16:44:24
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README.md

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                                     -# CoGAPS Version: 3.3.20
                                     +# CoGAPS Version: 3.3.22
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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added fixedPatterns option for normal CoGAPS

Tom Sherman authored on 19/12/2018 14:59:41
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README.md

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                                     -# CoGAPS Version: 3.3.15
                                     +# CoGAPS Version: 3.3.20
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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better parameter use

Tom Sherman authored on 23/11/2018 00:35:31
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README.md

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                                     -# CoGAPS Version: 3.3.14
                                     +# CoGAPS Version: 3.3.15
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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update version in readme

Tom Sherman authored on 16/11/2018 22:54:09
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README.md

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                                     -# CoGAPS Version: 3.3.13
                                     +# CoGAPS Version: 3.3.14
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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added worker print message when finished

Tom Sherman authored on 16/11/2018 21:15:25
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README.md

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                                     -# CoGAPS Version: 3.3.12
                                     +# CoGAPS Version: 3.3.13
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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bump version and update docs

Tom Sherman authored on 16/11/2018 17:48:32
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README.md

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                                     -# CoGAPS Version: 3.3.11
                                     +# CoGAPS Version: 3.3.12
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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version bump and update vignette

Tom Sherman authored on 15/11/2018 22:05:24
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README.md

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                                     -# CoGAPS Version: 3.3.10
                                     +# CoGAPS Version: 3.3.11
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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updated version

Tom Sherman authored on 15/11/2018 21:39:41
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README.md

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                                     -# CoGAPS Version: 3.3.9
                                     +# CoGAPS Version: 3.3.10
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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updated version & docs

Tom Sherman authored on 15/11/2018 21:12:14
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README.md

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                                     -# CoGAPS Version: 3.3.8
                                     +# CoGAPS Version: 3.3.9
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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updated docs and version

Tom Sherman authored on 15/11/2018 20:14:12
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README.md

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                                     -# CoGAPS Version: 3.3.7
                                     +# CoGAPS Version: 3.3.8
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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updated docs

Tom Sherman authored on 13/11/2018 19:47:40
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README.md

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                                     -# CoGAPS Version: 3.3.6
                                     +# CoGAPS Version: 3.3.7
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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updated docs & version

Tom Sherman authored on 12/11/2018 18:03:34
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README.md

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                                     -# CoGAPS Version: 3.3.5
                                     +# CoGAPS Version: 3.3.6
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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added helper function to build retina subset

Tom Sherman authored on 07/11/2018 23:17:33
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README.md

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                                     -# CoGAPS Version: 3.3.4
                                     +# CoGAPS Version: 3.3.5
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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fixed up tests

Tom Sherman authored on 07/11/2018 22:38:49
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README.md

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                                     -# CoGAPS Version: 3.3.3
                                     +# CoGAPS Version: 3.3.4
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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update README version

Tom Sherman authored on 05/11/2018 21:08:23
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README.md

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                                     -# CoGAPS Version: 3.2.3
                                     +# CoGAPS Version: 3.3.3
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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correct version

Tom Sherman authored on 05/11/2018 21:03:42
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README.md

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                                     -# CoGAPS Version: 3.3.2
                                     +# CoGAPS Version: 3.2.3
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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cleaned up version and regenerated vignette

Tom Sherman authored on 02/11/2018 20:05:05
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README.md

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                                     -# CoGAPS Version: 3.1.52
                                     +# CoGAPS Version: 3.3.2
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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passing check

Tom Sherman authored on 29/10/2018 22:48:29
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README.md

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                                     -# CoGAPS Version: 3.3.50
                                     +# CoGAPS Version: 3.1.52
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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updated git config so that permissions get committed

Tom Sherman authored on 29/10/2018 20:03:19
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README.md

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1	1	old mode 100644
2	2	new mode 100755

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restoring some tests

Tom Sherman authored on 22/10/2018 19:25:14
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README.md

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                                     -# CoGAPS Version: 3.3.24
                                     +# CoGAPS Version: 3.3.50
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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fixed bug where GWCoGAPS didn't return dimnames

Tom Sherman authored on 24/08/2018 01:28:09
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README.md

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                                     -# CoGAPS Version: 3.3.23
                                     +# CoGAPS Version: 3.3.24
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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version bump

Tom Sherman authored on 23/08/2018 20:09:04
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README.md

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                                     -# CoGAPS Version: 3.3.22
                                     +# CoGAPS Version: 3.3.23
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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version bump to 3.3.22

Tom Sherman authored on 23/08/2018 19:39:20
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README.md

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                                     -# CoGAPS Version: 3.3.21
                                     +# CoGAPS Version: 3.3.22
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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use a sorted vector for atomic domain

Tom Sherman authored on 23/08/2018 17:53:21
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README.md

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                                     -# CoGAPS Version: 3.3.11
                                     +# CoGAPS Version: 3.3.21
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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version bump

Tom Sherman authored on 15/08/2018 16:37:29
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README.md

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                                     -# CoGAPS Version: 3.3.10
                                     +# CoGAPS Version: 3.3.11
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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added lookup table for updating atom mass

Tom Sherman authored on 13/08/2018 15:18:30
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README.md

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                                     -# CoGAPS Version: 3.3.9
                                     +# CoGAPS Version: 3.3.10
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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updates

Tom Sherman authored on 09/08/2018 20:06:04
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README.md

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                                     -# CoGAPS Version: 3.3.8
                                     +# CoGAPS Version: 3.3.9
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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fixed checkpoints

Tom Sherman authored on 09/08/2018 16:44:08
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README.md

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                                     -# CoGAPS Version: 3.3.7
                                     +# CoGAPS Version: 3.3.8
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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fixed vignette and bumped version

Tom Sherman authored on 09/08/2018 00:12:30
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                                     -# CoGAPS Version: 3.3.6
                                     +# CoGAPS Version: 3.3.7
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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added more features to GWCoGAPS and scCoGAPS

Tom Sherman authored on 08/08/2018 22:34:56
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README.md

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                                     -# CoGAPS Version: 3.3.5
                                     +# CoGAPS Version: 3.3.6
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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saveUnmatchedPatterns added to wrappers; updated docs

Tom Sherman authored on 06/08/2018 19:30:00
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README.md

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                                     -# CoGAPS Version: 3.3.3
                                     +# CoGAPS Version: 3.3.5
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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docs

Tom Sherman authored on 06/08/2018 19:12:48
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README.md

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                                     -# CoGAPS Version: 3.3.2
                                     +# CoGAPS Version: 3.3.3
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

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updated readme'

Tom Sherman authored on 02/08/2018 19:53:11
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README.md

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                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)
                                      Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.
+                                    +
                                     +# Installing CoGAPS
+                                    +
                                     +*CoGAPS* is a bioconductor R package and so the release version can be installed
                                     +as follows:
+                                    +
                                     +```
                                     +source("https://bioconductor.org/biocLite.R")
                                     +biocLite("CoGAPS")
                                     +```
+                                    +
                                     +The most up-to-date version of *CoGAPS* can be installed directly from the
                                     +*FertigLab* Github Repository:
+                                    +
                                     +```
                                     +## Method 1 using biocLite
                                     +biocLite("FertigLab/CoGAPS", dependencies = TRUE, build_vignettes = TRUE)
+                                    +
                                     +## Method 2 using devtools package
                                     +devtools::install_github("FertigLab/CoGAPS")
                                     +```
+                                    +
                                     +There is also an option to install the development version of *CoGAPS*,
                                     +while this version has the latest experimental features, it is not guaranteed
                                     +to be stable.
+                                    +
                                     +```
                                     +## Method 1 using biocLite
                                     +biocLite("FertigLab/CoGAPS", ref="develop", dependencies = TRUE, build_vignettes = TRUE)
+                                    +
                                     +## Method 2 using devtools package
                                     +devtools::install_github("FertigLab/CoGAPS", ref="develop")
                                     +```
+                                    +
                                     +# Using CoGAPS
+                                    +
                                     +Follow the vignette here: http://htmlpreview.github.io/?https://github.com/FertigLab/CoGAPS/blob/develop/vignettes/CoGAPS.html
                                     \ No newline at end of file

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updated docs

Tom Sherman authored on 02/08/2018 19:41:24
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README.md

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                                     -# CoGAPS
                                     +# CoGAPS Version: 3.3.2
                                      [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                      [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)
                                     -[![Travis-CI Build Status](https://travis-ci.org/CoGAPS/CoGAPS.svg?branch=master)](https://travis-ci.org/CoGAPS/CoGAPS)
                                     -[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/CoGAPS/CoGAPS?branch=master&svg=true)](https://ci.appveyor.com/project/CoGAPS/CoGAPS)
                                     -[![Coverage Status](https://img.shields.io/codecov/c/github/CoGAPS/CoGAPS/master.svg)](https://codecov.io/github/CoGAPS/CoGAPS?branch=master)
+                                    -
                                      Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.

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added bioc logo and download stat to readme

sherman5 authored on 19/04/2018 16:24:04
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README.md

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                                      # CoGAPS
                                     +[![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)
                                     +[![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)
+                                    +
                                      [![Travis-CI Build Status](https://travis-ci.org/CoGAPS/CoGAPS.svg?branch=master)](https://travis-ci.org/CoGAPS/CoGAPS)
                                      [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/CoGAPS/CoGAPS?branch=master&svg=true)](https://ci.appveyor.com/project/CoGAPS/CoGAPS)
                                      [![Coverage Status](https://img.shields.io/codecov/c/github/CoGAPS/CoGAPS/master.svg)](https://codecov.io/github/CoGAPS/CoGAPS?branch=master)

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Add Codecov for tracking test coverage

Jacob Carey authored on 28/12/2015 18:18:56
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README.md

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                                      [![Travis-CI Build Status](https://travis-ci.org/CoGAPS/CoGAPS.svg?branch=master)](https://travis-ci.org/CoGAPS/CoGAPS)
                                      [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/CoGAPS/CoGAPS?branch=master&svg=true)](https://ci.appveyor.com/project/CoGAPS/CoGAPS)
                                     +[![Coverage Status](https://img.shields.io/codecov/c/github/CoGAPS/CoGAPS/master.svg)](https://codecov.io/github/CoGAPS/CoGAPS?branch=master)
                                      Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.

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Add AppVeyor for testing windows builds

Jacob Carey authored on 28/12/2015 14:54:46
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README.md

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                                      # CoGAPS
                                      [![Travis-CI Build Status](https://travis-ci.org/CoGAPS/CoGAPS.svg?branch=master)](https://travis-ci.org/CoGAPS/CoGAPS)
+                                    -
                                     +[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/CoGAPS/CoGAPS?branch=master&svg=true)](https://ci.appveyor.com/project/CoGAPS/CoGAPS)
                                      Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.

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Add Travis CI integration

Jacob Carey authored on 18/12/2015 21:13:40
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README.md

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                                      # CoGAPS
                                     +[![Travis-CI Build Status](https://travis-ci.org/CoGAPS/CoGAPS.svg?branch=master)](https://travis-ci.org/CoGAPS/CoGAPS)
+                                    +
+                                    +
                                      Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.

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Copy description from BioC to README

Jacob Carey authored on 18/12/2015 20:37:30
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README.md

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                                      # CoGAPS
+                                    +
                                     +Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.

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first commit

Jacob Carey authored on 18/12/2015 20:29:57
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README.md

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                                     +# CoGAPS