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ClustIRR

Clustering of immune receptor repertoires

https://github.com/snaketron/clustirr

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
    4 of 7 committers (57.1%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.9%) to scientific vocabulary

Keywords

b-cell-receptor bioinformatics clustering immunoinformatics immunology quantitative-methods rep-seq repertoire-analysis t-cell-receptor

Keywords from Contributors

immune-repertoire vdj-recombination tcr-repertoire immunological-bioinformatics bioconductor-package immunoglobulin immunogenomics immune-repertoire-analysis high-throughput-sequencing differential-gene-expression
Last synced: 9 months ago · JSON representation

Repository

Clustering of immune receptor repertoires

Basic Info
  • Host: GitHub
  • Owner: snaketron
  • License: gpl-3.0
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 42.8 MB
Statistics
  • Stars: 3
  • Watchers: 2
  • Forks: 0
  • Open Issues: 4
  • Releases: 0
Topics
b-cell-receptor bioinformatics clustering immunoinformatics immunology quantitative-methods rep-seq repertoire-analysis t-cell-receptor
Created about 3 years ago · Last pushed 9 months ago
Metadata Files
Readme License

README.md

ClustIRR: Clustering of Immune Receptor Repertoires

Build Status

Overview

ClustIRR analyzes repertoires of B- and T-cell receptors. It begins the analysis by identifying communities (i.e., specificity groups) of immune receptors with similar specificities, based on the sequences of their complementarity determining regions (CDRs). Next, it employs a Bayesian probabilistic models to quantify differential community occupancy (DCO) between repertoires, allowing the identification of expanding or contracting communities in response to factors such as infection or cancer treatment.

How to use ClustIRR

ClustIRR is an R-package available from Bioconductor:

https://bioconductor.org/packages/ClustIRR/

To install this package, start R and enter:

```r if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("ClustIRR") ```

To use the development version of ClustIRR you can install it from Github. To do this, start R and enter:

r library(devtools) install_github("snaketron/ClustIRR")

Case studies are provided in the directory /vignettes

Workflow & output

clustirr workflow

Owner

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

GitHub Events

Total
  • Issues event: 6
  • Watch event: 1
  • Delete event: 1
  • Issue comment event: 3
  • Push event: 73
  • Create event: 2
Last Year
  • Issues event: 6
  • Watch event: 1
  • Delete event: 1
  • Issue comment event: 3
  • Push event: 73
  • Create event: 2

Committers

Last synced: 11 months ago

All Time
  • Total Commits: 549
  • Total Committers: 7
  • Avg Commits per committer: 78.429
  • Development Distribution Score (DDS): 0.284
Past Year
  • Commits: 145
  • Committers: 4
  • Avg Commits per committer: 36.25
  • Development Distribution Score (DDS): 0.083
Top Committers
Name Email Commits
sktron s****i@u****e 393
Kai Wollek k****k@s****e 142
J Wokaty j****y@s****u 6
Kai Wollek k****k@w****e 3
sktron-vm240 s****i@g****m 2
A Wokaty a****y@s****u 2
Hervé Pagès h****b@g****m 1
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 2 stud.uni-duisburg-essen.de: 1 uni-due.de: 1

Issues and Pull Requests

Last synced: 9 months ago

All Time
  • Total issues: 37
  • Total pull requests: 0
  • Average time to close issues: 2 months
  • Average time to close pull requests: N/A
  • Total issue authors: 2
  • Total pull request authors: 0
  • Average comments per issue: 0.46
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 4
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • snaketron (18)
  • kaozkai (17)
Pull Request Authors
Top Labels
Issue Labels
documentation (9) enhancement (7) bioconductor guidelines (4) benchmarking (4) implementation (3) submission process (2) bug (2) question (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 4,625 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
  • Total maintainers: 1
bioconductor.org: ClustIRR

Clustering of immune receptor repertoires

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 4,625 Total
Rankings
Dependent repos count: 0.0%
Forks count: 30.1%
Dependent packages count: 31.7%
Stargazers count: 36.9%
Average: 39.5%
Downloads: 98.6%
Maintainers (1)
simokitanovski@gmail.com
Last synced: 9 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.3.0 depends
  • future * imports
  • future.apply * imports
  • igraph * imports
  • methods * imports
  • stats * imports
  • stringdist * imports
  • utils * imports
  • visNetwork * imports
  • BiocStyle * suggests
  • ggplot2 * suggests
  • ggrepel * suggests
  • knitr * suggests
  • patchwork * suggests
  • testthat * suggests