GenomicInteractions
R/Bioconductor package for handling Genomic interaction data, annotating genomic features with interaction information and producing summary plots / statistics
https://github.com/computationalregulatorygenomicsicl/genomicinteractions
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
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✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
1 of 13 committers (7.7%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.4%) to scientific vocabulary
Keywords from Contributors
Repository
R/Bioconductor package for handling Genomic interaction data, annotating genomic features with interaction information and producing summary plots / statistics
Basic Info
- Host: GitHub
- Owner: ComputationalRegulatoryGenomicsICL
- Language: R
- Default Branch: master
- Size: 4.37 MB
Statistics
- Stars: 7
- Watchers: 4
- Forks: 1
- Open Issues: 8
- Releases: 0
Metadata Files
README.md
GenomicInteractions
GenomicInteractions is an R/Bioconductor package for manipulating and investigating chromatin interaction data. It provides simple annotation of genomic features which interfaces with existing Bioconductor packages, as well as numerous plotting functions and summary statistics.
Installation
To install this package, start R and enter:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("GenomicInteractions")
To install the latest version from this repository using the devtools package:
library(devtools)
install_github("ComputationalRegulatoryGenomicsICL/GenomicInteractions")
Bioconductor links and documentation
The Bioconductor page contains documentation for the current release.
To view example Hi-C and ChIA-PET analysis for using this package on your system, start R and enter:
browseVignettes("GenomicInteractions")
Citation
From within R, enter citation("GenomicInteractions"):
``` Harmston, N., Ing-Simmons, E., Perry, M., Baresic, A. and Lenhard, B. (2015). GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data. BMC Genomics 16:963.
A BibTeX entry for LaTeX users is
@Article{, title = {GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data}, author = {Nathan Harmston and Elizabeth Ing-Simmons and Malcolm Perry and Anja Bare{\v{s}}i{\'{c}} and Boris Lenhard}, year = {2015}, journal = {BMC Genomics}, volume = {16}, issue = {963}, doi = {10.1186/s12864-015-2140-x}, url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-2140-x}, } ```
Contributing
We welcome contributions in any form: suggestions, issues, bugfixes. Pull requests should be made to the development branch.
Owner
- Name: ComputationalRegulatoryGenomicsICL
- Login: ComputationalRegulatoryGenomicsICL
- Kind: organization
- Repositories: 13
- Profile: https://github.com/ComputationalRegulatoryGenomicsICL
GitHub Events
Total
- Fork event: 1
Last Year
- Fork event: 1
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Nathan Harmston | n****7@c****k | 33 |
| Liz Ing-Simmons | l****s@g****m | 24 |
| Herve Pages | h****s@f****g | 14 |
| Nitesh Turaga | n****a@g****m | 12 |
| Dan Tenenbaum | d****a@f****g | 11 |
| Hervé Pagès | h****s@f****g | 4 |
| Hervé Pagès | h****b@g****m | 2 |
| vobencha | v****n@r****g | 2 |
| vobencha | v****a@g****m | 2 |
| LiNk-NY | m****9@g****m | 1 |
| Marc Carlson | m****n@f****g | 1 |
| Nathaniel Hayden | n****n@f****g | 1 |
| Steve Pederson | s****d | 1 |
Committer Domains (Top 20 + Academic)
Packages
- Total packages: 1
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Total downloads:
- bioconductor 55,872 total
- Total dependent packages: 7
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: GenomicInteractions
Utilities for handling genomic interaction data
- Homepage: https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/GenomicInteractions/inst/doc/GenomicInteractions.pdf
- License: GPL-3
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Latest release: 1.42.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- InteractionSet * depends
- R >= 3.5 depends
- Biobase * imports
- BiocGenerics >= 0.15.3 imports
- GenomeInfoDb * imports
- GenomicRanges >= 1.29.6 imports
- Gviz * imports
- IRanges * imports
- Rsamtools * imports
- S4Vectors >= 0.13.13 imports
- data.table * imports
- dplyr * imports
- ggplot2 * imports
- grDevices * imports
- graphics * imports
- grid * imports
- gridExtra * imports
- igraph * imports
- methods * imports
- rtracklayer * imports
- stats * imports
- stringr * imports
- utils * imports
- BiocStyle * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests