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IgGeneUsage

Comparison of gene usage in immune repertoires under different biological conditions

https://github.com/snaketron/iggeneusage

Science Score: 10.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 7 committers (28.6%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.4%) to scientific vocabulary

Keywords

b-cell-receptor bcr-repertoire differential-analysis differential-gene-expression high-throughput-sequencing immune-repertoire immune-repertoire-analysis immune-repertoires immunogenomics immunoglobulin immunoinformatics immunological-bioinformatics immunology tcr-repertoire vdj-recombination

Keywords from Contributors

gene bioconductor-packages bioinformatics grna-sequence genomics sequencing proteomics ontologies human-cell-atlas tidyverse
Last synced: 6 months ago · JSON representation

Repository

Comparison of gene usage in immune repertoires under different biological conditions

Basic Info
  • Host: GitHub
  • Owner: snaketron
  • License: mit
  • Language: R
  • Default Branch: master
  • Size: 281 MB
Statistics
  • Stars: 6
  • Watchers: 2
  • Forks: 1
  • Open Issues: 0
  • Releases: 1
Topics
b-cell-receptor bcr-repertoire differential-analysis differential-gene-expression high-throughput-sequencing immune-repertoire immune-repertoire-analysis immune-repertoires immunogenomics immunoglobulin immunoinformatics immunological-bioinformatics immunology tcr-repertoire vdj-recombination
Created over 6 years ago · Last pushed 11 months ago
Metadata Files
Readme License

README.md

IgGeneUsage Logo

Lifecycle: stable
codecov

Overview

IgGeneUsage: computational tool for the analysis of differential gene usage (DGU) in B- and T-cell receptor repertoires.

For more information see vignettes in folder vignette/.

alt text

Owner

  • Name: snaketron
  • Login: snaketron
  • Kind: user

GitHub Events

Total
  • Delete event: 1
  • Push event: 2
  • Pull request event: 1
  • Create event: 2
Last Year
  • Delete event: 1
  • Push event: 2
  • Pull request event: 1
  • Create event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 505
  • Total Committers: 7
  • Avg Commits per committer: 72.143
  • Development Distribution Score (DDS): 0.133
Past Year
  • Commits: 78
  • Committers: 4
  • Avg Commits per committer: 19.5
  • Development Distribution Score (DDS): 0.128
Top Committers
Name Email Commits
sktron s****i@u****e 438
snaketron s****n 44
Nitesh Turaga n****a@g****m 12
sktron-vm240 s****i@g****m 6
J Wokaty j****y@s****u 2
J Wokaty j****y 2
Hervé Pagès h****b@g****m 1
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 1 uni-due.de: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 13
  • Total pull requests: 2
  • Average time to close issues: almost 2 years
  • Average time to close pull requests: 1 day
  • Total issue authors: 3
  • Total pull request authors: 2
  • Average comments per issue: 0.54
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 6 minutes
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • snaketron (10)
  • vjcitn (2)
  • ghost (1)
Pull Request Authors
  • snaketron (2)
  • andrjohns (1)
Top Labels
Issue Labels
enhancement (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 9,181 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: IgGeneUsage

Differential gene usage in immune repertoires

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 9,181 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Stargazers count: 14.9%
Forks count: 18.4%
Average: 22.2%
Downloads: 77.7%
Maintainers (1)
simo.kitanovski@uni-due.de
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.6.0 depends
  • Rcpp >= 0.12.0 depends
  • StanHeaders > 2.18.1 depends
  • SummarizedExperiment * depends
  • methods * depends
  • reshape2 >= 1.4.3 imports
  • rstan >= 2.19.2 imports
  • BiocStyle * suggests
  • ggforce * suggests
  • ggplot2 * suggests
  • ggrepel * suggests
  • gridExtra * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat >= 2.1.0 suggests
.github/workflows/r.yml actions
  • actions/checkout v2 composite
  • actions/upload-artifact main composite
  • r-lib/actions/check-r-package v1 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
  • r-lib/actions/setup-r-dependencies v1 composite