Package: scRepertoire 2.1.0
scRepertoire: A toolkit for single-cell immune receptor profiling
scRepertoire is a toolkit for processing and analyzing single-cell T-cell receptor (TCR) and immunoglobulin (Ig). The scRepertoire framework supports use of 10x, AIRR, BD, MiXCR, Omniscope, TRUST4, and WAT3R single-cell formats. The functionality includes basic clonal analyses, repertoire summaries, distance-based clustering and interaction with the popular Seurat and SingleCellExperiment/Bioconductor R workflows.
Authors:
scRepertoire_2.1.0.tar.gz
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scRepertoire/json (API)
NEWS
# Install 'scRepertoire' in R: |
install.packages('scRepertoire', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ncborcherding/screpertoire/issues
- contig_list - A list of 8 single-cell T cell receptor sequences runs.
- mini_contig_list - Processed subset of 'contig_list'
- scRep_example - A Seurat object of 500 single T cells,
On BioConductor:scRepertoire-2.1.0(bioc 3.20)scRepertoire-2.0.0(bioc 3.19)
Last updated 2 months agofrom:9061c35380
Exports:addVariablealluvialClonesclonalAbundanceclonalBiasclonalClusterclonalCompareclonalDiversityclonalHomeostasisclonalLengthclonalNetworkclonalOccupyclonalOverlapclonalOverlayclonalProportionclonalQuantclonalRarefactionclonalScatterclonalSizeDistributioncombineBCRcombineExpressioncombineTCRcreateHTOContigListexportClonesgetCirclizehighlightClonesloadContigspercentAApercentGenespercentKmerpercentVJpositionalEntropypositionalPropertyStartracDiversitysubsetClonesvizGenes
Dependencies:abindaskpassBiobaseBiocGenericscachemclicodetoolscolorspacecpp11crayoncubaturecurlDelayedArraydigestdotCall64dplyrevdevmixfansifarverfastmapfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggalluvialggdendroggforceggplot2ggraphggrepelglobalsgluegraphlayoutsgridExtragslgtablehashhttrigraphiNEXTIRangesisobandjsonlitelabelinglatticelazyevallifecyclelistenvmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmimemunsellnlmeopensslparallellypillarpkgconfigplyrpolyclipprogressrpurrrquantregR6RColorBrewerRcppRcppArmadilloRcppEigenreshape2rjsonrlangS4ArraysS4VectorsscalesSeuratObjectSingleCellExperimentspspamSparseArraySparseMstringdiststringistringrSummarizedExperimentsurvivalsyssystemfontstibbletidygraphtidyrtidyselecttruncdisttweenrUCSC.utilsutf8vctrsVGAMviridisviridisLitewithrXVectorzlibbioc