Package index • AnalyzAIRR

All functions

AnalyzAIRR: AnalyzAIRR - AIRR-compliant R package for the analysis of bulk Ig/TCR repertoire datasets

CalcDissimilarity(): Calculation of repertoire dissimilarities

Intervals(): Calculation of the clonal distribution per interval

RepSeqData: RepSeqData

ShannonNorm(): Shannon normalization of repertoires

countFeatures(): Computing the occurrence of any repertoire level

diffExpGroup(): Differential expression analysis

diffExpInd(): Differential expression analysis between two samples

diversityIndices(): Calculation of diversity indices

dropSamples(): Exclude repertoires from a RepSeqExperiment object.

filterCount(): Filtering based on sequence count

filterSequence(): Exclude a sequence from a RepSeqExperiment object.

generalizedDiversity(): Computation of the Renyi or the Hill index

getPrivate(): Extract private sequences

getProductive(): Extract productive sequences

getPublic(): Extract public sequences

getTopSequences(): Extract the most frequent sequences

getUnproductive(): Extract unproductive sequences

mergeRepSeq(): Merge RepSeqExperiment objects

perturbationScore(): Calculation of the perturbation score

plotColors(): Color palette

plotDiffExp(): Visualization of differential expression in a volcano plot

plotDissHeatmap(): Visualization of repertoire dissimilarities in a heatmap

plotDissMDS(): Visualization of repertoire dissimilarities in a multidimensional scaling (MDS) plot

plotDissimilarity(): Visualization of repertoire dissimilarities

plotDiversity(): Visualization of the diversity indices

plotGenDiversity(): Visualization of the Hill or Renyi profiles

plotGeneUsage(): Compare V or J gene distributions

plotIndGeneUsage(): Visualization of the V or J gene usage

plotIndIntervals(): Visualization of the clonal distribution per interval in a single sample

plotIndMap(): Visualization of a repertoire structure through a circular treemap

plotIndStatistics(): Visualization of basic or diversity statistics for one sample

plotIntervals(): Visualization of the clonal distribution per interval

plotRankDistrib(): Visualization of the clonal distribution as a function of the rank

plotRarefaction(): Visualization of the rarefaction curves

plotRenyiIndex(): Visualization of the Renyi index

plotScatter(): Visualization of the inter-repertoire sharing on a scatter plot

plotStatScatter(): Visualization of basic statistics in a scatter plot

plotStatistics(): Visualization of basic statistics

plotVenn(): Visualization of the inter-repertoire sharing on an Venn diagram

readAIRRSet(): Building of a RepSeqExperiment object

readFormatSet(): An alternative method for the building of a RepSeqExperiment object

renyiIndex(): Computation of the Renyi index

sampleRepSeqExp(): Down-sampling of repertoires

theme_RepSeq(): A theme for the visualization plots