Package: AllelicImbalance 1.45.0

Jesper R Gadin

AllelicImbalance: Investigates Allele Specific Expression

Provides a framework for allelic specific expression investigation using RNA-seq data.

Authors:Jesper R Gadin, Lasse Folkersen

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AllelicImbalance.pdf |AllelicImbalance.html✨
AllelicImbalance/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/pappewaio/allelicimbalance/issues

Datasets:

On BioConductor:AllelicImbalance-1.43.0(bioc 3.20)AllelicImbalance-1.42.0(bioc 3.19)

geneticsinfrastructuresequencing

4.78 score 6 scripts 364 downloads 111 exports 153 dependencies

Last updated 23 days agofrom:ffd47ab9c9. Checks:OK: 6 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winOKOct 30 2024
R-4.5-linuxOKOct 30 2024
R-4.4-winOKOct 30 2024
R-4.4-macOKOct 30 2024
R-4.3-winOKOct 30 2024
R-4.3-macNOTEOct 30 2024

Exports:alleleCountsalleleCounts<-altalt<-altExistannotationBarplotaqualsaquals<-arankASEDAnnotationTrackASEsetFromArraysASEsetFromBamASEsetFromCountListbarplotbarplotLatticeCountsbarplotLatticeFractionbasicbinom.testchisq.testcountAllelesFromBamcountsPerSamplecountsPerSnpCoverageDataTrackcoverageMatrixListFromGALdecorateWithExonsdecorateWithGenesdefaultMapBiasdefaultPhasedetectAIdetectedAI_vs_threshold_variable_multigraph_plotdetectedAI_vs_threshold_variable_plotdetectedAI_vs_threshold_variable_summaryDetectedAIFromArrayfractionfractionPlotDffrequencyfrequency_vs_threshold_variable_multigraph_plotfrequency_vs_threshold_variable_plotfrequency_vs_threshold_variable_summaryGAnalysisgbagbarplotgenotypegenotype<-genotype2phasegetAlleleCountsgetAlleleQualitygetAnnotationDataFramegetAreaFromGeneNamesgetCDSFromAnnotationgetCDSVectorgetDefaultMapBiasExpMeangetDefaultMapBiasExpMean3DgetExonsFromAnnotationgetExonsVectorgetGenesFromAnnotationgetGenesVectorgetSnpIdFromLocationgetTranscriptsFromAnnotationgetTranscriptsVectorglocationplothetFiltimpBamGALimpBamGRLimpBcfGRimpBcfGRLimplodeList.oldinferAllelesinferAltAlleleinferGenotypeslegendBarplotlocationplotlvalva.internalmakeMaskedFastamapBiasmapBias<-mapBiasRefmaternalAlleleminCountFiltminFreqFiltmultiAllelicFiltpaternalAllelephasephase<-phase2genotypephaseArray2phaseMatrixphaseMatrix2ArrayplotpvaluerandomRefrealCigarPosition.oldrealCigarPositions.oldrealCigarPositionsList.oldrefref<-refAllelereference_frequency_density_vs_threshold_variable_multigraph_plotreference_frequency_density_vs_threshold_variable_plotreferenceFrequencyrefExistregionSummaryRiskVariantFromGRangesAndPhaseArrayscanForHeterozygotesscanForHeterozygotes.oldsumnamesthresholdCountSamplethresholdDeltaFrequencythresholdFrequencythresholdPvalueusedSNPs_vs_threshold_variable_summary

Dependencies:abindade4AnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpixmappkgconfigplogrpngprettyunitsprogressProtGenericspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessegmentedseqinrsnowspSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc

AllelicImbalance Vignette

Jesper R. Gadin and Lasse Folkersen

Rendered fromAllelicImbalance-vignette.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2017-04-29
Started: 2015-03-16

Readme and manuals

Help Manual

Help pageTopics
A package meant to provide all basic functions for high-throughput allele specific expression analysisAllelicImbalance-package AllelicImbalance
AnnotationDb wrappersannotation-wrappers getAnnotationDataFrame getCDSFromAnnotation getCDSVector getExonsFromAnnotation getExonsVector getGenesFromAnnotation getGenesVector getTranscriptsFromAnnotation getTranscriptsVector
add annotation to AllelicImbalance barplotannotationBarplot
barplot ASEset objectsASEset-barplot barplot barplot,ASEset-method
ASEset objectsalleleCounts alleleCounts,ASEset-method alleleCounts<- alleleCounts<-,ASEset-method alt alt,ASEset-method alt<- alt<-,ASEset,ANY-method altExist altExist,ASEset-method aquals aquals,ASEset-method aquals<- aquals<-,ASEset-method arank arank,ASEset-method ASEset ASEset-class countsPerSample countsPerSample,ASEset-method countsPerSnp countsPerSnp,ASEset-method fraction fraction,ASEset-method frequency frequency,ASEset-method genotype genotype,ASEset-method genotype<- genotype<-,ASEset-method mapBias mapBias,ASEset-method mapBias<- mapBias<-,ASEset-method maternalAllele maternalAllele,ASEset-method paternalAllele paternalAllele,ASEset-method phase phase,ASEset-method phase<- phase<-,ASEset-method ref ref,ASEset-method ref<- ref<-,ASEset,ANY-method refExist refExist,ASEset-method
genotype filter methodsASEset-filters hetFilt hetFilt,ASEset-method
gbarplot ASEset objectsASEset-gbarplot gbarplot gbarplot,ASEset-method
glocationplot ASEset objectsASEset-glocationplot glocationplot glocationplot,ASEset-method
ASEset-gviztrack ASEset objectsASEDAnnotationTrack ASEDAnnotationTrack,ASEset-method ASEset-gviztrack CoverageDataTrack CoverageDataTrack,ASEset-method
locationplot ASEset objectsASEset-locationplot locationplot locationplot,ASEset-method
scanForHeterozygotesASEset-scanForHeterozygotes scanForHeterozygotes scanForHeterozygotes,ASEset-method scanForHeterozygotes,GAlignmentsList-method
ASEset.old objectASEset.old
ASEset.sim objectASEset.sim
ASEset from bam fileASEsetFromBam ASEsetFromBam,GRanges-method
lattice barplot inner functions for ASEset objectsbarplot-lattice-support barplotLatticeCounts barplotLatticeFraction
binomial testbinom.test binom.test,ASEset-method
chi-square testchisq.test chisq.test,ASEset-method
alleleCounts from bam filecountAllelesFromBam countAllelesFromBam,GRanges-method
coverage matrix of GAlignmentsListcoverageMatrixListFromGAL coverageMatrixListFromGAL,GAlignmentsList-method
Generate default mapbias from genotypedefaultMapBias defaultMapBias,ASEset-method
defaultPhasedefaultPhase defaultPhase,numeric-method
detectAIdetectAI detectAI,ASEset-method
DetectedAI classDetectedAI DetectedAI-class DetectedAI-method referenceFrequency referenceFrequency,DetectedAI-method thresholdCountSample thresholdCountSample,DetectedAI-method thresholdDeltaFrequency thresholdDeltaFrequency,DetectedAI-method thresholdFrequency thresholdFrequency,DetectedAI-method thresholdPvalue thresholdPvalue,DetectedAI-method
DetectedAI plotDetectedAI-plot detectedAI_vs_threshold_variable_multigraph_plot detectedAI_vs_threshold_variable_multigraph_plot,DetectedAI-method detectedAI_vs_threshold_variable_plot detectedAI_vs_threshold_variable_plot,DetectedAI-method frequency_vs_threshold_variable_multigraph_plot frequency_vs_threshold_variable_multigraph_plot,DetectedAI-method frequency_vs_threshold_variable_plot frequency_vs_threshold_variable_plot,DetectedAI-class frequency_vs_threshold_variable_plot,DetectedAI-method reference_frequency_density_vs_threshold_variable_multigraph_plot reference_frequency_density_vs_threshold_variable_multigraph_plot,DetectedAI-method reference_frequency_density_vs_threshold_variable_plot reference_frequency_density_vs_threshold_variable_plot,DetectedAI-method
DetectedAI summaryDetectedAI-summary detectedAI_vs_threshold_variable_summary detectedAI_vs_threshold_variable_summary,DetectedAI-method frequency_vs_threshold_variable_summary frequency_vs_threshold_variable_summary,DetectedAI-method usedSNPs_vs_threshold_variable_summary usedSNPs_vs_threshold_variable_summary,DetectedAI-method
Plot DataframefractionPlotDf fractionPlotDf,ASEset-method
global analysis wrappergba gba,character-method
genomatrix objectgenomatrix
genotype2phasegenotype2phase genotype2phase,matrix-method
snp count datagetAlleleCounts getAlleleCounts,GAlignmentsList-method
snp quality datagetAlleleQuality getAlleleQuality,GAlignmentsList-method
Get Gene AreagetAreaFromGeneNames getAreaFromGeneNames,character-method
Map BiasgetDefaultMapBiasExpMean getDefaultMapBiasExpMean,ANY-method getDefaultMapBiasExpMean,list-method getDefaultMapBiasExpMean3D getDefaultMapBiasExpMean3D,ANY-method
Get rsIDs from locations of SNPgetSnpIdFromLocation getSnpIdFromLocation,GRanges-method
GlobalAnalysis classGlobalAnalysis GlobalAnalysis-class GlobalAnalysis-method
GRvariants objectGRvariants
histogram plotshist hist,ASEset-method hist,ReferenceBias-method histplot
implode list of arguments into environmentimplodeList.old
Import BamimpBamGAL impBamGAL,character-method import-bam
Import Bam-2impBamGRL impBamGRL.old import-bam-2
Import Bcf SelectionimpBcfGR impBcfGR,character-method impBcfGRL impBcfGRL,character-method import-bcf
inference of SNPs of ASEsetinferAlleles inferAlleles,ASEset-method
inferAltAlleleinferAltAllele inferAltAllele,ASEset-method
infererence of genotypes from ASEset count datainferGenotypes inferGenotypes,ASEset-method
Initialize ASEsetASEsetFromArrays ASEsetFromCountList initialize-ASEset
Initialize DetectedAIDetectedAIFromArray initialize-DetectedAI
Initialize GlobalAnalysisGAnalysis initialize-GlobalAnalysis
Initialize RiskVariantinitialize-RiskVariant RiskVariantFromGRangesAndPhaseArray
add legend to AllelicImbalance barplotlegendBarplot
LinkVariantAlmlof classLinkVariantAlmlof LinkVariantAlmlof-class LinkVariantAlmlof-method pvalue pvalue,LinkVariantAlmlof-method
plot LinkVariantAlmlof objectsLinkVariantAlmlof-plot plot plot,LinkVariantAlmlof,ANY-method plot,LinkVariantAlmlof-method
lvalva lva,array-method lva,ASEset-method
lva.internallva.internal lva.internal,array-method
makes masked fasta referencemakeMaskedFasta makeMaskedFasta,character-method
mapBias for reference allelemapBiasRef mapBiasRef,ASEset-method
minCountFilt methodsminCountFilt minCountFilt,ASEset-method
minFreqFilt methodsminFreqFilt minfreqFilt minFreqFilt,ASEset-method
multi-allelic filter methodsmultiAllelicFilt multiAllelicFilt,ASEset-method
phase2genotypephase2genotype phase2genotype,array-method
phaseArray2phaseMatrixphaseArray2phaseMatrix phaseArray2phaseMatrix,array-method
phaseMatrix2ArrayphaseMatrix2Array phaseMatrix2Array,matrix-method
Random ref allele from genotyperandomRef randomRef,ASEset-method
reads objectreads
Reference allelerefAllele refAllele,ASEset-method
regionSummaryregionSummary regionSummary,ASEset-method regionSummary,numeric-method
RegionSummary classbasic basic,RegionSummary-method RegionSummary RegionSummary-class RegionSummary-method sumnames sumnames,RegionSummary-method
RiskVariant classalt,RiskVariant-method alt<-,RiskVariant,ANY-method phase,RiskVariant-method phase<-,RiskVariant-method ref,RiskVariant-method ref<-,RiskVariant,ANY-method RiskVariant RiskVariant-class RiskVariant-method
scanForHeterozygotes-oldscanForHeterozygotes.old