https://github.com/fertiglab/ataccogaps
Science Score: 13.0%
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○CITATION.cff file
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✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
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○Scientific vocabulary similarity
Low similarity (5.2%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: FertigLab
- Language: R
- Default Branch: master
- Size: 77.2 MB
Statistics
- Stars: 4
- Watchers: 5
- Forks: 1
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
ATACCoGAPS
Package which provides tools for processing and analysis of single-cell ATAC-seq data with the Bayesian Non-Negative Matrix Factorization algorithm, CoGAPS, as described in our Nucleic Acids Research paper https://doi.org/10.1093/nar/gkaa349.
Install ATACCoGAPS with:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ATACCoGAPS")
A tutorial demonstrating the standard analysis pipeline for ATACCoGAPS using data from Schep et al, 2017 can be found here: https://rossinerbe.github.io/ATACCoGAPS_Tutorial
Owner
- Name: FertigLab
- Login: FertigLab
- Kind: organization
- Email: ejfertig@jhmi.edu
- Repositories: 68
- Profile: https://github.com/FertigLab
Software projects in computational biology and bioinformatics in Elana Fertig's lab in Oncology Biostatistics and Bioinformatics at JHMI
GitHub Events
Total
- Push event: 3
Last Year
- Push event: 3
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| rossinerbe | r****e@g****m | 68 |
| rossinerbe | 4****e | 22 |
Dependencies
- CoGAPS >= 3.5.13 depends
- R >= 4.2.0 depends
- BSgenome.Hsapiens.UCSC.hg19 * imports
- BSgenome.Mmusculus.UCSC.mm10 * imports
- GeneOverlap * imports
- GenomicFeatures * imports
- GenomicRanges * imports
- Homo.sapiens * imports
- IRanges * imports
- JASPAR2016 * imports
- Mus.musculus * imports
- TFBSTools * imports
- chromVAR * imports
- dplyr * imports
- fgsea * imports
- gplots * imports
- gtools * imports
- motifmatchr * imports
- msigdbr * imports
- projectR * imports
- rGREAT * imports
- stringr * imports
- tidyverse * imports
- knitr * suggests
- viridis * suggests