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83 limit number of cores for tests #84

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merged 15 commits into from
Feb 8, 2024
Merged

83 limit number of cores for tests #84

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4118fd6
bump x.y.z version to even y prior to creation of RELEASE_3_18 branch
jwokaty Oct 24, 2023
b0c6417
bump x.y.z version to odd y following creation of RELEASE_3_18 branch
jwokaty Oct 24, 2023
a75556d
merge and bump
dimalvovs Feb 1, 2024
01b94a8
Update r-build-check.yml
dimalvovs Feb 1, 2024
c024b37
add BiocFileCache
dimalvovs Feb 1, 2024
063d45c
try replace line endings
dimalvovs Feb 1, 2024
8fbffb3
merge grom github
dimalvovs Feb 1, 2024
0d193ba
try replacing eol again
dimalvovs Feb 1, 2024
b73930e
Update r-build-check.yml
dimalvovs Feb 1, 2024
9db07ca
Update README.md
dimalvovs Feb 2, 2024
ac465af
Update README.md
dimalvovs Feb 2, 2024
2e85d21
Update README.md
dimalvovs Feb 2, 2024
5e4855d
Update README.md
dimalvovs Feb 2, 2024
7039826
Update README.md
dimalvovs Feb 2, 2024
9ad7c25
Update README.md
dimalvovs Feb 2, 2024
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4 changes: 3 additions & 1 deletion .github/workflows/r-build-check.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,4 +5,6 @@ on:
workflow_dispatch:
jobs:
build-check:
uses: FertigLab/actions/.github/workflows/r-build-check.yml@v1
uses: FertigLab/actions/.github/workflows/r-build-check.yml@v1.1.1
with:
chargs: 'c("--no-manual")'
7 changes: 4 additions & 3 deletions DESCRIPTION
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@@ -1,6 +1,6 @@
Package: CoGAPS
Version: 3.21.6
Date: 2023-03-18
Version: 3.23.1
Date: 2024-02-01
Title: Coordinated Gene Activity in Pattern Sets
Author: Jeanette Johnson, Ashley Tsang, Jacob Mitchell, Thomas Sherman, Wai-shing Lee, Conor Kelton, Ondrej Maxian, Jacob Carey,
Genevieve Stein-O'Brien, Michael Considine, Maggie Wodicka, John Stansfield,
Expand Down Expand Up @@ -44,7 +44,8 @@ Suggests:
knitr,
rmarkdown,
BiocStyle,
SeuratObject
SeuratObject,
BiocFileCache
LinkingTo: Rcpp, BH
VignetteBuilder: knitr
LazyLoad: true
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5 changes: 3 additions & 2 deletions README.md
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@@ -1,10 +1,11 @@
<img src="https://user-images.githubusercontent.com/25310425/169565420-56958b50-29a2-4032-afb3-08447577d074.png" width="300">
<img src="https://user-images.githubusercontent.com/25310425/169565420-56958b50-29a2-4032-afb3-08447577d074.png" width="150">

[![R build status](https://github.com/FertigLab/CoGAPS/workflows/r-build-check/badge.svg)](https://github.com/FertigLab/CoGAPS/actions?workflow=r-build-check)

# 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/)
[![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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