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pathview

pathway based data integration and visualization

https://github.com/datapplab/pathview

Science Score: 26.0%

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    CITATION.cff file
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    DOI references
    Found 3 DOI reference(s) in README
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    Scientific vocabulary similarity
    Low similarity (15.2%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

pathway based data integration and visualization

Basic Info
  • Host: GitHub
  • Owner: datapplab
  • Language: R
  • Default Branch: master
  • Size: 3.29 MB
Statistics
  • Stars: 41
  • Watchers: 3
  • Forks: 17
  • Open Issues: 21
  • Releases: 0
Created almost 6 years ago · Last pushed over 1 year ago
Metadata Files
Readme

README.md

pathview R package

Overview

Pathview is a leading tool for pathway based data integration and visualization. It maps, integrates and renders a wide variety of biological data on relevant pathway graphs. Pathview has 3 important features: * Interpretable graphs with publication quality: KEGG view for easy interpretation and Graphviz view for better graphical control. * Strong data integration capacity. It works with: 1) all data mappable to pathways, 2) 30 of molecular ID types (genes/protein, compound/metabolite), 3) 10000+ species, 4) various data attributes and formats. * Simple and powerful: fully automated and error-resistant, seamlessly integrates with a wide range of pathway and gene set (enrichment) analysis tools.

Citation

Please cite the Pathview paper when using this open-source package. This will help the project and our team:

Luo W, Brouwer C. Pathview: an R/Biocondutor package for pathway-based data integration and visualization. Bioinformatics, 2013, 29(14):1830-1831, doi: 10.1093/bioinformatics/btt285

Installation (within R)

``` r

install from BioConductor

if(!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("pathview")

Or the development version from GitHub:

install.packages("devtools")

devtools::install_github("datapplab/pathview") ```

Quick start with demo data (R code)

Note Pathview focuses on KEGG pathways, which is good for most regular analyses. If you are interested in working with other major pathway databases, including Reactome, MetaCyc, SMPDB, PANTHER, METACROP etc, you can use SBGNview. Please check the quick start page and the main tutorial for details.

r library(pathview) data(gse16873.d) pv.out <- pathview(gene.data = gse16873.d[, 1], pathway.id = "04110", species = "hsa", out.suffix = "gse16873")

More information

Please check the BioC page for tutorials and extra documentations.

Also see the Pathview Web server for interactive GUI with example graphics.

Thank you for your interest.

Owner

  • Name: datapplab
  • Login: datapplab
  • Kind: organization

GitHub Events

Total
  • Issues event: 2
  • Watch event: 3
  • Issue comment event: 1
  • Push event: 1
  • Pull request event: 3
  • Fork event: 1
Last Year
  • Issues event: 2
  • Watch event: 3
  • Issue comment event: 1
  • Push event: 1
  • Pull request event: 3
  • Fork event: 1

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 12
  • Total Committers: 3
  • Avg Commits per committer: 4.0
  • Development Distribution Score (DDS): 0.25
Past Year
  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Weijun Luo l****n@y****m 9
weijun w****n@d****1 2
Javad Noorbakhsh j****b 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 31
  • Total pull requests: 4
  • Average time to close issues: 6 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 31
  • Total pull request authors: 2
  • Average comments per issue: 2.1
  • Average comments per pull request: 1.25
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: 10 minutes
  • Issue authors: 3
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.33
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • whiteorchid (1)
  • jordlang01 (1)
  • lumotroph (1)
  • hilariodc (1)
  • ivokwee (1)
  • sjtuyf (1)
  • RMasteling (1)
  • emrahkirdok (1)
  • silvtal (1)
  • eggrandio (1)
  • iszhi (1)
  • Asa12138 (1)
  • Elseedy28 (1)
  • alhadjil (1)
  • nvelden (1)
Pull Request Authors
  • AJBassa (3)
  • javadnoorb (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 606,578 total
  • Total dependent packages: 9
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: pathview

a tool set for pathway based data integration and visualization

  • Versions: 5
  • Dependent Packages: 9
  • Dependent Repositories: 0
  • Downloads: 606,578 Total
Rankings
Dependent repos count: 0.0%
Downloads: 3.9%
Average: 3.9%
Forks count: 4.0%
Dependent packages count: 5.5%
Stargazers count: 6.2%
Maintainers (1)
luo_weijun@yahoo.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 2.10 depends
  • AnnotationDbi * imports
  • KEGGREST * imports
  • KEGGgraph * imports
  • Rgraphviz * imports
  • XML * imports
  • graph * imports
  • methods * imports
  • org.Hs.eg.db * imports
  • png * imports
  • utils * imports
  • BiocGenerics * suggests
  • RUnit * suggests
  • gage * suggests
  • org.Mm.eg.db * suggests