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seq2pathway

A union of mapping genomic loci to genes and testing genes for enriched pathways

https://github.com/xyang2uchicago/seq2pathway

Science Score: 18.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
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    codemeta.json file
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    .zenodo.json file
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    DOI references
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    Academic publication links
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    Scientific vocabulary similarity
    Low similarity (2.7%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

A union of mapping genomic loci to genes and testing genes for enriched pathways

Basic Info
  • Host: GitHub
  • Owner: xyang2uchicago
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 8.62 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 7 years ago · Last pushed about 5 years ago
Metadata Files
Readme Citation

README.md

seq2pathway

Seq2pathway can be used to seach for enriched functional pre-defined gene-sets (at pathway level), using variable next-generation sequencing data (rather than gene lists). Integral to this tool are the 'seq2gene' and 'gene2pathway' components in series that infer a quantitative pathway profiles for each sample.

Owner

  • Name: YangGroup
  • Login: xyang2uchicago
  • Kind: user
  • Location: Chicago
  • Company: the University of Chicago

Citation (CITATION) 

citEntry(entry="Article",
  author ="Wang B, Cunningham JM, Yang XH",
title ="Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data",
  journal =      "Bioinformatics",
  volume =       " ",
  year =         "2015", 
  pages =        "3043-5",
  url =          "http://bioinformatics.oxfordjournals.org/content/early/2015/05/27/bioinformatics.btv289.full",
  textVersion = paste(
 "Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation ",
 "sequencing data", "Wang B, Cunningham JM, Yang XH",
  "2015, Bioinformatics. Sep; 31(18):3043-5")
)

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Dependencies

DESCRIPTION cran
  • R >= 3.6.2 depends
  • GSA * imports
  • GenomicRanges * imports
  • WGCNA * imports
  • biomaRt * imports
  • nnet * imports
  • seq2pathway.data * imports