Package: tadar 1.3.1

Lachlan Baer

tadar: Transcriptome Analysis of Differential Allelic Representation

This package provides functions to standardise the analysis of Differential Allelic Representation (DAR). DAR compromises the integrity of Differential Expression analysis results as it can bias expression, influencing the classification of genes (or transcripts) as being differentially expressed. DAR analysis results in an easy-to-interpret value between 0 and 1 for each genetic feature of interest, where 0 represents identical allelic representation and 1 represents complete diversity. This metric can be used to identify features prone to false-positive calls in Differential Expression analysis, and can be leveraged with statistical methods to alleviate the impact of such artefacts on RNA-seq data.

Authors:Lachlan Baer [aut, cre], Stevie Pederson [aut]

tadar_1.3.1.tar.gz
tadar_1.3.1.zip(r-4.5)tadar_1.3.1.zip(r-4.4)tadar_1.3.1.zip(r-4.3)
tadar_1.3.1.tgz(r-4.4-any)tadar_1.3.1.tgz(r-4.3-any)
tadar_1.3.1.tar.gz(r-4.5-noble)tadar_1.3.1.tar.gz(r-4.4-noble)
tadar_1.3.1.tgz(r-4.4-emscripten)tadar_1.3.1.tgz(r-4.3-emscripten)
tadar.pdf |tadar.html✨
tadar/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/baerlachlan/tadar/issues

Datasets:

On BioConductor:tadar-1.3.0(bioc 3.20)tadar-1.2.0(bioc 3.19)

bioconductor-package

10 exports 1.45 score 147 dependencies

Last updated 27 days agofrom:6acb35e78e

Exports:assignFeatureDarcountAllelescountsToPropsdarfilterLociflipRangesplotChrDarplotDarECDFreadGenotypesunphaseGT

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrpngprettyunitsprogressProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc

Differential Allelic Representation (DAR) analysis

Lachlan Baer, Stevie Pederson

Rendered fromdar.Rmdusingknitr::rmarkdownon Jun 14 2024.

Last update: 2023-10-16
Started: 2023-03-29

Readme and manuals

Help Manual

Help pageTopics
Assign DAR values to genomic featuresassignFeatureDar assignFeatureDar,GRangesList,GRanges-method
Genomic feature example datachr1_genes
Count alleles within each experimental groupcountAlleles countAlleles,GRanges,list-method
Convert allele counts to proportionscountsToProps countsToProps,GRangesList-method
Calculate Differential Allelic Representation (DAR)dar dar,GRangesList,matrix-method
Filter locifilterLoci filterLoci,GRangesList-method
Convert DAR origin ranges to DAR region ranges, or vice versaflipRanges flipRanges,GRangesList-method
Plot DAR across a chromosomeplotChrDar plotChrDar,GRanges-method
Plot the Empirical Cumulative Distribution Function of DARplotDarECDF plotDarECDF,GRanges-method
Read genotypes from a VCF filereadGenotypes readGenotypes,character-method readGenotypes,TabixFile-method
Unphase genotypesunphaseGT unphaseGT,data.frame-method unphaseGT,matrix-method