chromswitch
An R/Bioconductor package for detecting chromatin state switches
Science Score: 13.0%
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Found 4 DOI reference(s) in README -
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Low similarity (9.2%) to scientific vocabulary
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Repository
An R/Bioconductor package for detecting chromatin state switches
Basic Info
- Host: GitHub
- Owner: sjessa
- License: other
- Language: R
- Default Branch: master
- Homepage: https://bioconductor.org/packages/chromswitch
- Size: 1.72 MB
Statistics
- Stars: 3
- Watchers: 2
- Forks: 1
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
chromswitch: An R/Bioconductor package for detecting chromatin state switches
chromswitch implements a flexible method to detect chromatin state
switches between samples in two biological conditions in a specific genomic
region of interest given peaks or chromatin state calls from ChIP-seq data.
NOTE: chromswitch is now deprecated: https://bioconductor.org/packages/3.17/bioc/html/chromswitch.html
Method
The chromswitch paper is now published Bioinformatics:
Selin Jessa, Claudia L Kleinman (2018). chromswitch: a flexible method to detect chromatin state switches, Bioinformatics, https://doi.org/10.1093/bioinformatics/bty075
For details on the method, see the Supplementary Methods.
Installation
~chromswitch is available from Bioconductor at bioconductor.org/packages/chromswitch. To install the package from the R console:~
The chromswitch BioConductor package is now deprecated.
r
install.packages("BiocManager")
BiocManager::install("chromswitch")
For an introduction to the package, check out the vignette, or open it from the R console:
browseVignettes("chromswitch")
Issues
Bug reports and issues are welcome, please open an issue in the GitHub repository.
Owner
- Name: Selin Jessa
- Login: sjessa
- Kind: user
- Location: Montreal
- Company: @fungenomics at McGill University
- Website: selinjessa.com
- Twitter: selinjessa
- Repositories: 5
- Profile: https://github.com/sjessa
Computational biologist, completing my PhD in Quantitative Life Sciences: interested in the brain, functional genomics, and open science.
GitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| sjessa | s****a@g****m | 134 |
| Nitesh Turaga | n****a@g****m | 10 |
| Hervé Pagès | h****s@f****g | 4 |
| vobencha | v****n@r****g | 2 |
| vobencha | v****a@g****m | 2 |
| Kayla-Morrell | k****l@r****g | 1 |
| Selin Jessa | s****a@s****n | 1 |
Committer Domains (Top 20 + Academic)
Packages
- Total packages: 1
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Total downloads:
- bioconductor 7,335 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 1
- Total maintainers: 1
bioconductor.org: chromswitch
An R package to detect chromatin state switches from epigenomic data
- Homepage: https://github.com/sjessa/chromswitch
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/chromswitch/inst/doc/chromswitch.pdf
- License: MIT + file LICENSE
- Status: removed
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Latest release: 1.22.0
published over 2 years ago