Package: IgGeneUsage 1.26.0

Simo Kitanovski

IgGeneUsage: Differential gene usage in immune repertoires

Detection of biases in the usage of immunoglobulin (Ig) genes is an important task in immune repertoire profiling. IgGeneUsage detects aberrant Ig gene usage between biological conditions using a probabilistic model which is analyzed computationally by Bayes inference. With this IgGeneUsage also avoids some common problems related to the current practice of null-hypothesis significance testing.

Authors:Simo Kitanovski [aut, cre]

IgGeneUsage_1.26.0.tar.gz
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IgGeneUsage_1.26.0.tgz(r-4.6-x86_64)IgGeneUsage_1.26.0.tgz(r-4.6-arm64)IgGeneUsage_1.26.0.tgz(r-4.5-x86_64)IgGeneUsage_1.26.0.tgz(r-4.5-arm64)
IgGeneUsage_1.26.0.tar.gz(r-4.7-arm64)IgGeneUsage_1.26.0.tar.gz(r-4.7-x86_64)IgGeneUsage_1.26.0.tar.gz(r-4.6-arm64)IgGeneUsage_1.26.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
IgGeneUsage/json (API)
NEWS

# Install 'IgGeneUsage' in R:
install.packages('IgGeneUsage', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/snaketron/iggeneusage/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • CDR3_Epitopes - Net charge usage in CDR3 sequences of T-cell receptor repertoires disturbed by Influenza-A and CMV
  • d_zibb_1 - Simulated Ig gene usage data
  • d_zibb_2 - Simulated Ig gene usage data
  • d_zibb_3 - Simulated Ig gene usage data
  • d_zibb_4 - Simulated Ig gene usage data
  • d_zibb_5 - Simulated Ig gene usage data
  • d_zibb_6 - Simulated Ig gene usage data
  • Ig - IGHV gene family usage in vaccine-challenged B-cell repertoires
  • Ig_SE - IGHV gene family usage in vaccine-challenged B-cell repertoires
  • IGHV_HCV - IGHV gene usage in HCV+ and healthy individuals

On BioConductor:IgGeneUsage-1.27.0(bioc 3.24)IgGeneUsage-1.26.0(bioc 3.23)

differentialexpressionregressiongeneticsbayesianbiomedicalinformaticsimmunooncologymathematicalbiologyb-cell-receptorbcr-repertoiredifferential-analysisdifferential-gene-expressionhigh-throughput-sequencingimmune-repertoireimmune-repertoire-analysisimmune-repertoiresimmunogenomicsimmunoglobulinimmunoinformaticsimmunological-bioinformaticsimmunologytcr-repertoirevdj-recombinationcpp

5.38 score 6 stars 1 scripts 332 downloads 2 exports 69 dependencies

Last updated from:08fbf37464 (on RELEASE_3_23). Checks:12 NOTE, 1 OK, 1 FAIL. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE442
linux-devel-arm64NOTE801
linux-devel-x86_64NOTE910
source / vignettesOK944
linux-release-arm64NOTE795
linux-release-x86_64NOTE896
macos-release-arm64NOTE486
macos-release-x86_64NOTE1264
macos-oldrel-arm64NOTE497
macos-oldrel-x86_64NOTE1620
windows-develNOTE1267
windows-releaseNOTE1020
windows-oldrelNOTE867
wasm-releaseFAIL168

Exports:DGULOO

Dependencies:abindbackportsBHBiobaseBiocGenericscallrcheckmateclicpp11DelayedArraydescdistributionaldplyrfarvergenericsGenomicRangesggplot2gluegridExtragtableinlineIRangesisobandlabelinglatticelifecycleloomagrittrMatrixMatrixGenericsmatrixStatsnumDerivpillarpkgbuildpkgconfigplyrposteriorprocessxpspurrrQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelreshape2rlangrstanrstantoolsS4ArraysS4VectorsS7scalesSeqinfoSparseArrayStanHeadersstringistringrSummarizedExperimenttensorAtibbletidyrtidyselectutf8vctrsviridisLitewithrXVector

User Manual: IgGeneUsage

SK

Rendered fromUser_Manual.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2024-04-05
Started: 2022-10-17