pathlinkR
Analysis and visualization of RNA-Seq results
Science Score: 39.0%
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✓DOI references
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○Scientific vocabulary similarity
Low similarity (17.4%) to scientific vocabulary
Keywords
Repository
Analysis and visualization of RNA-Seq results
Basic Info
- Host: GitHub
- Owner: hancockinformatics
- License: gpl-3.0
- Language: R
- Default Branch: devel
- Homepage: https://hancockinformatics.github.io/pathlinkR/
- Size: 17.6 MB
Statistics
- Stars: 30
- Watchers: 1
- Forks: 1
- Open Issues: 0
- Releases: 4
Topics
Metadata Files
README.md
pathlinkR 
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Overview
pathlinkR is an R package designed to facilitate analysis DE genes produced from of RNA-Seq experiments. Our aim with pathlinkR is to provide a number of functions/tools which can be applied to list(s) of DE genes, to help the user obtain biological insights into their results, and produce publication-ready figures to summarize these findings.
Check out our article in PLOS Computational Biology: https://doi.org/10.1371/journal.pcbi.1012422
Installation
pathlinkR can be installed from this Github repository via devtools, or from Bioconductor as follows: ```r
Github development
devtools::install_github("https://github.com/hancockinformatics/pathlinkR")
Bioconductor release
BiocManager::install("pathlinkR")
Bioconductor develelopment
BiocManager::install("pathlinkR", version="devel") ```
Workflow & functions
The functions provided in pathlinkR can be grouped into a number of different general approaches:
- Direct visualization of differential expression results:
- Volcano plots to show the transcriptomic changes in a single condition
- Heatmaps to compare fold changes of groups of genes across multiple conditions
- Protein-Protein Interaction (PPI) network creation and visualization, leveraging curated interaction data from InnateDB
- A combined interface to multiple pathway enrichment tools, including
Reactome pathways and
MSigDB Hallmark
gene sets
- Simple yet effective plots to summarize and compare these findings across multiple conditions
- Pathway enrichment results can also be visualized as a network of connected pathways, with the option for static or interactive output
See the vignette for an example workflow including each of the included functions, and more details on the included methods and how they may be used.
Contributors
pathlinkR was created and developed by Andy An & Travis Blimkie at the CMDR REW Hancock Lab.
Versioning
This package follows Bioconductor's guidelines on version numbering; more information can be found here.
License
This project uses the GNU General Public License v3.0, available here.
Owner
- Name: Hancock Lab
- Login: hancockinformatics
- Kind: organization
- Location: Canada
- Website: http://cmdr.ubc.ca/bobh/
- Repositories: 4
- Profile: https://github.com/hancockinformatics
GitHub Events
Total
- Create event: 6
- Issues event: 2
- Release event: 3
- Watch event: 17
- Delete event: 2
- Issue comment event: 5
- Push event: 15
- Pull request review event: 1
- Pull request event: 2
- Fork event: 1
Last Year
- Create event: 6
- Issues event: 2
- Release event: 3
- Watch event: 17
- Delete event: 2
- Issue comment event: 5
- Push event: 15
- Pull request review event: 1
- Pull request event: 2
- Fork event: 1
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 2
- Total pull requests: 17
- Average time to close issues: 12 days
- Average time to close pull requests: about 3 hours
- Total issue authors: 2
- Total pull request authors: 1
- Average comments per issue: 6.0
- Average comments per pull request: 0.0
- Merged pull requests: 17
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 1
- Average time to close issues: 12 days
- Average time to close pull requests: about 19 hours
- Issue authors: 2
- Pull request authors: 1
- Average comments per issue: 6.0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Navin-tamil (1)
- 146107576 (1)
Pull Request Authors
- travis-m-blimkie (23)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 4,631 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 4
- Total maintainers: 1
bioconductor.org: pathlinkR
Analyze and interpret RNA-Seq results
- Homepage: https://github.com/hancockinformatics/pathlinkR
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/pathlinkR/inst/doc/pathlinkR.pdf
- License: GPL-3 + file LICENSE
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Latest release: 1.4.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout v3 composite
- r-lib/actions/check-r-package v2 composite
- r-lib/actions/setup-pandoc v2 composite
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- actions/checkout v3 composite
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- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
- R >= 4.2.0 depends
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- SteinerNet * imports
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