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'))

Peer review:

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-1.19.0(bioc 3.20)IgGeneUsage-1.18.0(bioc 3.19)

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

6.19 score 6 stars 1 scripts 143 downloads 2 exports 85 dependencies

Last updated 23 days agofrom:63e09a3399. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-win-x86_64NOTEOct 30 2024
R-4.5-linux-x86_64NOTEOct 30 2024
R-4.4-win-x86_64NOTEOct 31 2024
R-4.4-mac-x86_64NOTEOct 31 2024
R-4.4-mac-aarch64NOTEOct 31 2024
R-4.3-win-x86_64NOTEOct 31 2024
R-4.3-mac-x86_64NOTEOct 31 2024
R-4.3-mac-aarch64NOTEOct 31 2024

Exports:DGULOO

Dependencies:abindaskpassbackportsBHBiobaseBiocGenericscallrcheckmateclicolorspacecpp11crayoncurlDelayedArraydescdistributionaldplyrfansifarvergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragtablehttrinlineIRangesisobandjsonlitelabelinglatticelifecycleloomagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmenumDerivopensslpillarpkgbuildpkgconfigplyrposteriorprocessxpspurrrQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelreshape2rlangrstanrstantoolsS4ArraysS4VectorsscalesSparseArrayStanHeadersstringistringrSummarizedExperimentsystensorAtibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

User Manual: IgGeneUsage

SK

Rendered fromUser_Manual.Rmdusingknitr::rmarkdownon Oct 30 2024.

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