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RIVER

R package for RIVER (RNA-Informed Variant Effect on Regulation)

https://github.com/ipw012/river

Science Score: 23.0%

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

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    CITATION.cff file
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    codemeta.json file
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    .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
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    Academic publication links
    Links to: biorxiv.org, nature.com
  • ○
    Committers with academic emails
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    Scientific vocabulary similarity
    Low similarity (10.8%) to scientific vocabulary

Keywords

bayesian biomedicalinformatics clustering functional-variants functionalgenomics functionalprediction generegulation genetics geneticvariability genomicvariation snp systemsbiology transcription transcriptomevariant transcriptomics variant
Last synced: 6 months ago · JSON representation

Repository

R package for RIVER (RNA-Informed Variant Effect on Regulation)

Basic Info
  • Host: GitHub
  • Owner: ipw012
  • Language: R
  • Default Branch: master
  • Size: 2.79 MB
Statistics
  • Stars: 12
  • Watchers: 3
  • Forks: 4
  • Open Issues: 2
  • Releases: 0
Topics
bayesian biomedicalinformatics clustering functional-variants functionalgenomics functionalprediction generegulation genetics geneticvariability genomicvariation snp systemsbiology transcription transcriptomevariant transcriptomics variant
Created about 9 years ago · Last pushed almost 6 years ago
Metadata Files
Readme

README.md

Status: Travis CI Travis-CI Build Status

RIVER

RIVER is an R package of a probabilistic modeling framework, RIVER (RNA-Informed Variant Effect on Regulation) that jointly analyzes personal genome (WGS) and transcriptome data (RNA-seq) to estimate the probability that a variant has regulatory impact in that individual. It is based on a generative model assuming that genomic annotations, such as the location of a variant with respect to regulatory elements, determine the prior probability that variant is a functional regulatory variant, which is an unobserved variable. The functional regulatory variant status then influences whether nearby genes are likely to display outlier levels of gene expression in that person. RIVER is trained in an unsupervised manner such that it does not require a labeled set of functional/non-functional variants; rather it derives its predictive power from identifying expression patterns that tend to coincide with particular rare variant annotations.

For more information about RIVER, check the vignettes.

For further details of a list of genomic annotations used for constructing features and how to generate the features and outlier status, please refer to our submitted publication.

Installation

Get most recent version of R (>= 3.4) from CRAN.

```R

try http:// if https:// URLs are not supported

source("http://bioconductor.org/biocLite.R") biocLite("RIVER") ```

Vignettes

The vignettes for this package can be viewed via Bioconductor's website (manual backup).

Citation

Below is the citation output from using citation('RIVER') in R. Please run this yourself to check for any updates on how to cite RIVER.

To cite the RIVER package in publications use:

Li, X , Kim, Y , Tsang, EK , Davis, JR , Damani, FN, Chiang, C, Hess, GT, Zappala, Z, Strober, BJ, Scott, AJ, Li, A, Ganna, A, Bassik, MC, Merker, J, GTEx Consortium, Hall, IM, Battle, A , Montgomery, SB , "The impact of rare variation on gene expression across tissues", Nature 550, 239-243 (2017), doi:10.1038/nature24267, .

Testing

Testing on Bioc-devel is feasible thanks to R Travis as well as Bioconductor's nightly build.

Owner

  • Name: Yungil Kim
  • Login: ipw012
  • Kind: user
  • Location: New York, USA
  • Company: Icahn School of Medicine at Mt. Sinai

GitHub Events

Total
  • Watch event: 2
Last Year
  • Watch event: 2

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 32
  • Total Committers: 2
  • Avg Commits per committer: 16.0
  • Development Distribution Score (DDS): 0.188
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Yungil Kim i****2@g****m 26
Yungil Kim i****2 6

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 1
  • Total pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 1.0
  • 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
  • jeinson (1)
Pull Request Authors
  • lcolladotor (1)
Top Labels
Issue Labels
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Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 13,780 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: RIVER

R package for RIVER (RNA-Informed Variant Effect on Regulation)

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 13,780 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 20.6%
Downloads: 61.9%
Maintainers (1)
ipw012@gmail.com
Last synced: 6 months ago