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liger

Lightweight Iterative Gene set Enrichment in R

https://github.com/jefworks/liger

Science Score: 20.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    2 of 2 committers (100.0%) from academic institutions
  • ○
    Institutional organization owner
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (10.0%) to scientific vocabulary

Keywords

bioinformatics cran enrichment gene-sets gsea pathway-enrichment-analysis rstats
Last synced: 11 months ago · JSON representation

Repository

Lightweight Iterative Gene set Enrichment in R

Basic Info
Statistics
  • Stars: 56
  • Watchers: 5
  • Forks: 9
  • Open Issues: 1
  • Releases: 0
Topics
bioinformatics cran enrichment gene-sets gsea pathway-enrichment-analysis rstats
Created almost 11 years ago · Last pushed almost 2 years ago
Metadata Files
Readme License

README.md

Note: This package is no longer maintained as I no longer actively use it myself. For gene set enrichment analysis in R, please check out instead fgsea or clusterProfiler. I hope this repo and its vignettes may still be useful as resource for understanding such gene set enrichment analysis.

Lightweight Iterative Gene set Enrichment in R (LIGER)

R-CMD-check CRAN DOI

Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states. The original algorithm is detailed in Subramanian, Tamayo, et al. with Java implementations available through the Broad Institute.

The liger package provides a lightweight R implementation of this enrichment test on a list of values. Given a list of values, such as p-values or log-fold changes derived from differential expression analysis or other analyses comparing biological states, this package enables you to test a priori defined set of genes for enrichment to enable interpretability of highly significant or high fold-change genes.

Tutorials

Sample plots

Testing individual gene sets

```

gsea(values=vals, geneset=gs, mc.cores=1, plot=TRUE) ```

Testing multiple gene sets

```

ptm <- proc.time() bulk.gsea(vals, org.Hs.GO2Symbol.list[1:10]) p.val q.val sscore edge GO:0000002 0.00009999 0.0000000 2.6139724 70.912194 GO:0000003 0.25647435 0.4074000 0.5400972 13.170093 GO:0000012 0.24347565 0.4074000 0.5550191 8.392397 GO:0000014 0.13428657 0.3779000 0.6906745 -4.458762 GO:0000018 0.14448555 0.7215200 -0.6498716 11.111976 GO:0000022 0.33446655 0.8023667 -0.5014560 -11.015244 proc.time() - ptm user system elapsed 6.200 0.065 6.414 ```

```

ptm <- proc.time() iterative.bulk.gsea(values=vals, set.list=org.Hs.GO2Symbol.list[1:10]) p.val q.val sscore edge GO:0000002 0.00009999 0.00000 2.6054741 70.912194 GO:0000003 0.25867413 0.41730 0.5352656 13.170093 GO:0000012 0.24727527 0.41730 0.5545500 8.392397 GO:0000014 0.14128587 0.40300 0.6903051 -4.458762 GO:0000018 0.13988601 0.72684 -0.6485933 11.111976 GO:0000022 0.31666833 0.81440 -0.4975180 -11.015244 proc.time() - ptm user system elapsed 11.250 0.107 5.320 ```

Install

```

The easiest way to get liger is to install it from CRAN:

install.packages("liger")

Or get the latest development version from GitHub:

require(devtools) devtools::install_github("JEFworks/liger") ```

Contributing

We welcome any bug reports, enhancement requests, and other contributions. To submit a bug report or enhancement request, please use the liger GitHub issues tracker. For more substantial contributions, please fork this repo, push your changes to your fork, and submit a pull request with a good commit message.

Owner

  • Name: Jean Fan
  • Login: JEFworks
  • Kind: user
  • Location: Baltimore, MD
  • Company: Johns Hopkins University

Assistant Professor in the Center for Computational Biology, Department of Biomedical Engineering at JHU.

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 53
  • Total Committers: 2
  • Avg Commits per committer: 26.5
  • Development Distribution Score (DDS): 0.245
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
JEFworks j****n@f****u 40
JEFworks j****n@j****u 13
Committer Domains (Top 20 + Academic)
jhu.edu: 1 fas.harvard.edu: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 5
  • Total pull requests: 1
  • Average time to close issues: about 1 year
  • Average time to close pull requests: almost 3 years
  • Total issue authors: 5
  • Total pull request authors: 1
  • Average comments per issue: 2.4
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • 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
  • rivers-yao (1)
  • teng-gao (1)
  • slowkow (1)
  • samuel-marsh (1)
  • JEFworks (1)
Pull Request Authors
  • yihui (2)
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels

Packages

  • Total packages: 3
  • Total downloads:
    • cran 419 last-month
  • Total docker downloads: 11,222
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 4
    (may contain duplicates)
  • Total versions: 6
  • Total maintainers: 1
proxy.golang.org: github.com/jefworks/liger
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.7%
Dependent repos count: 5.8%
Last synced: 11 months ago
proxy.golang.org: github.com/JEFworks/liger
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.7%
Dependent repos count: 5.8%
Last synced: 11 months ago
cran.r-project.org: liger

Lightweight Iterative Geneset Enrichment

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 4
  • Downloads: 419 Last month
  • Docker Downloads: 11,222
Rankings
Stargazers count: 6.1%
Forks count: 6.3%
Dependent repos count: 14.6%
Average: 17.3%
Downloads: 23.3%
Docker downloads count: 24.9%
Dependent packages count: 28.8%
Maintainers (1)
jeanfan@jhu.edu
Last synced: about 1 year ago

Dependencies

DESCRIPTION cran
  • R >= 2.10 depends
  • Rcpp * imports
  • graphics * imports
  • matrixStats * imports
  • parallel * imports
  • stats * imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests