Package: IgGeneUsage 1.21.0

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_1.21.0.tar.gz
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IgGeneUsage.pdf |IgGeneUsage.html✨
IgGeneUsage/json (API)
NEWS

# Install 'IgGeneUsage' in R:
install.packages('IgGeneUsage', repos = c('https://bioc.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
  • IGHV_HCV - IGHV gene usage in HCV+ and healthy individuals
  • Ig - IGHV gene family usage in vaccine-challenged B-cell repertoires
  • Ig_SE - IGHV gene family usage in vaccine-challenged B-cell repertoires
  • 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

On BioConductor:IgGeneUsage-1.21.0(bioc 3.21)IgGeneUsage-1.20.0(bioc 3.20)

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

6.03 score 6 stars 1 scripts 183 downloads 2 exports 84 dependencies

Last updated 4 months agofrom:63e09a3399. Checks:1 OK, 8 NOTE, 2 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 01 2025
R-4.5-win-x86_64NOTEFeb 01 2025
R-4.5-mac-x86_64WARNINGFeb 01 2025
R-4.5-mac-aarch64WARNINGFeb 01 2025
R-4.5-linux-x86_64NOTEFeb 01 2025
R-4.4-win-x86_64NOTEFeb 01 2025
R-4.4-mac-x86_64NOTEFeb 01 2025
R-4.4-mac-aarch64NOTEFeb 01 2025
R-4.3-win-x86_64NOTEFeb 01 2025
R-4.3-mac-x86_64NOTEFeb 01 2025
R-4.3-mac-aarch64NOTEFeb 01 2025

Exports:DGULOO

Dependencies:abindaskpassbackportsBHBiobaseBiocGenericscallrcheckmateclicolorspacecpp11crayoncurlDelayedArraydescdistributionaldplyrfansifarvergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragtablehttrinlineIRangesisobandjsonlitelabelinglatticelifecycleloomagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmenumDerivopensslpillarpkgbuildpkgconfigplyrposteriorprocessxpspurrrQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelreshape2rlangrstanrstantoolsS4ArraysS4VectorsscalesSparseArrayStanHeadersstringistringrSummarizedExperimentsystensorAtibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVector

User Manual: IgGeneUsage

SK

Rendered fromUser_Manual.Rmdusingknitr::rmarkdownon Feb 01 2025.

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