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ATACseqTFEA

https://github.com/jianhong/atacseqtfea

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 4 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.8%) to scientific vocabulary

Keywords from Contributors

bioinformatics bioconductor-package
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: jianhong
  • Language: R
  • Default Branch: devel
  • Size: 4.33 MB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 4 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog

README.md

ATACseqTFEA

platforms build

Transcription Factor Enrichment Analysis for ATAC-seq

Assay for Transpose-Accessible Chromatin using sequencing (ATAC-seq) is a technique to assess genome-wide chromatin accessibility by probing open chromatin with hyperactive mutant Tn5 Transposase that inserts sequencing adapters into open regions of the genome. ATACseqTFEA is a improvement of current computational method that detects differential activity of transcription factors (TFs). ATACseqTFEA not only use the difference of open region information, but also (or emphasize) the difference of TFs footprints (cutting sites or insertion sites).

ATACseqTFEA provides an easy, rigorous way to broadly assess TF activity changes between two conditions.

schematic diagram of ATACseqTFEA

Installation

To install this package, start R and enter:

r library(BiocManager) BiocManager::install("ATACseqTFEA")

Documentation

To view documentation of ATACseqTFEA, start R and enter: r browseVignettes("ATACseqTFEA")

Contributions and Support

If you would like to contribute to this package, the standard workflow is as follows:

  1. Check that there isn't already an issue about your idea in the jianhong/ATACseqTFEA/issues to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
  2. Fork the jianhong/ATACseqTFEA to your GitHub account
  3. Make the necessary changes / additions within your forked repository following Bioconductor contribution
  4. Use devtools::build and devtools::check to check the package work properly.
  5. Submit a Pull Request against the master or current RELEASE_VERSION branch and wait for the code to be reviewed and merged

If you're not used to this workflow with git, you can start with some docs from GitHub or even their excellent git resources.

For further information or help, don't hesitate to get in touch on the Bioconductor support site.

Reporting bug/issues

Many thanks for taking an interest in improving Bioconductor package ATACseqTFEA. Please report bug/issues at jianhong/ATACseqTFEA/issues.

Owner

  • Name: JIANHONG OU
  • Login: jianhong
  • Kind: user

GitHub Events

Total
  • Watch event: 1
  • Push event: 3
Last Year
  • Watch event: 1
  • Push event: 3

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 36
  • Total Committers: 4
  • Avg Commits per committer: 9.0
  • Development Distribution Score (DDS): 0.306
Past Year
  • Commits: 7
  • Committers: 3
  • Avg Commits per committer: 2.333
  • Development Distribution Score (DDS): 0.571
Top Committers
Name Email Commits
JIANHONG OU j****g 25
Jianhong Ou j****u@J****l 7
J Wokaty j****y 2
J Wokaty j****y@s****u 2
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 5,902 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: ATACseqTFEA

Transcription Factor Enrichment Analysis for ATAC-seq

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 5,902 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 28.3%
Downloads: 85.0%
Maintainers (1)
jou@morgridge.org
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.2 depends
  • BiocGenerics * imports
  • GenomeInfoDb * imports
  • GenomicAlignments * imports
  • GenomicRanges * imports
  • IRanges * imports
  • Matrix * imports
  • Rsamtools * imports
  • S4Vectors * imports
  • SummarizedExperiment * imports
  • TFBSTools * imports
  • dplyr * imports
  • ggplot2 * imports
  • ggrepel * imports
  • limma * imports
  • methods * imports
  • motifmatchr * imports
  • pracma * imports
  • stats * imports
  • ATACseqQC * suggests
  • BSgenome.Drerio.UCSC.danRer10 * suggests
  • BiocStyle * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests