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GSALightning

GSALightning: Ultra-Fast Permutation-based Gene Set Analysis

https://github.com/billyhw/gsalightning

Science Score: 13.0%

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Last synced: 11 months ago · JSON representation

Repository

GSALightning: Ultra-Fast Permutation-based Gene Set Analysis

Basic Info
  • Host: GitHub
  • Owner: billyhw
  • License: gpl-2.0
  • Language: R
  • Default Branch: master
  • Size: 78.3 MB
Statistics
  • Stars: 5
  • Watchers: 0
  • Forks: 0
  • Open Issues: 1
  • Releases: 0
Created almost 11 years ago · Last pushed about 9 years ago

https://github.com/billyhw/GSALightning/blob/master/ 

[![Build Status](https://travis-ci.org/billyhw/GSALightning.svg?branch=master)](https://travis-ci.org/billyhw/GSALightning)
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[![codecov](https://codecov.io/gh/billyhw/GSALightning/branch/master/graph/badge.svg)](https://codecov.io/gh/billyhw/GSALightning)

## Motivation

GSA-Lightning is an R package that provides a fast implementation of permutation-based gene set
analysis for two-sample problem. This package is particularly useful when testing
simultaneously a large number of gene sets, or when a large number of permutations
is necessary for more accurate p-values estimation.

## Installation

GSA-Lightning requires R 3.3.0 or above (https://www.r-project.org/).

We recommend using the R "devtools" package to install GSALightning from Github.

To install devtools, in an R prompt type:

```{r}
install.packages("devtools")
```

To use devtools to install GSA-Lightning, type:

```{r}
devtools::install_github("billyhw/GSALightning")
```

Since the package contains some large example gene expression data sets, the download time may take 1-3 minutes. Please kindly be patient.

If the R vignette is also desired, use instead:

```{r}
library(devtools)
install_github("billyhw/GSALightning", build_vignette = TRUE)
```

Note the vignette will take some time to build (4-5 minutes) due to some large-scale analysis examples included in the vignette.

The Bioconductor stable release of GSA-Lightning is at:

https://bioconductor.org/packages/release/bioc/html/GSALightning.html

## Code

Please consult the R help page of GSA-Lightning for examples:

```{r}
? GSALight
```

## Contributor

Billy Heung Wing Chang (billyheungwing@gmail.com)

## Reference

Billy Heung Wing Chang and Weidong Tian (2016) GSA-Lightning: Ultra-fast Permutation-based Gene Set Analysis. Bioinformatics. doi: 10.1093/bioinformatics/btw349

http://bioinformatics.oxfordjournals.org/content/early/2016/06/11/bioinformatics.btw349.abstract

## License

GPL (>=2)

Owner

  • Name: Billy Chang
  • Login: billyhw
  • Kind: user

GitHub Events

Total
Last Year

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 171
  • Total Committers: 2
  • Avg Commits per committer: 85.5
  • Development Distribution Score (DDS): 0.222
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
billyhw b****g@g****m 133
billyhw b****g@y****a 38
Committer Domains (Top 20 + Academic)
yahoo.ca: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 3
  • Total pull requests: 23
  • Average time to close issues: 3 months
  • Average time to close pull requests: 8 days
  • Total issue authors: 2
  • Total pull request authors: 1
  • Average comments per issue: 0.67
  • Average comments per pull request: 0.0
  • Merged pull requests: 22
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • billyhw (2)
  • sinjia7 (1)
Pull Request Authors
  • billyhw (23)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 14,048 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: GSALightning

Fast Permutation-based Gene Set Analysis

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 14,048 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 19.5%
Downloads: 58.6%
Maintainers (1)
billyheungwing@gmail.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.3.0 depends
  • GSA * imports
  • Matrix * imports
  • data.table * imports
  • samr * imports
  • stats * imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests