ncborcherding/scRepertoire
A toolkit for single-cell immune receptor profiling

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A toolkit for single-cell immune receptor profiling

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.github/.gitignore
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.github/workflows/pkgdown.yaml
.github/workflows/pr-commands.yaml
.github/workflows/test-coverage.yaml
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DESCRIPTION
LICENSE
NAMESPACE
NEWS.md R/RcppExports.R R/addVariable.R R/alluvialClones.R R/clonalAbundance.R R/clonalBias.R R/clonalCluster.R R/clonalCompare.R R/clonalDiversity.R R/clonalHomeostasis.R R/clonalLength.R R/clonalNetwork.R R/clonalOccupy.R R/clonalOverlap.R R/clonalOverlay.R R/clonalProportion.R R/clonalQuant.R R/clonalRarefaction.R R/clonalScatter.R R/clonalSizeDistribution.R R/combineContigs.R R/combineExpression.R R/createHTOContigList.R R/data.R R/exportClones.R R/getCircilize.R R/global.R R/highlightClones.R R/loadContigs.R R/percentAA.R R/percentGenes.R R/percentKmer.R R/percentVJ.R R/positionalEntropy.R R/positionalProperty.R R/scRepertoire-package.R R/seurat_command.R R/startracDiversity.R R/subsetClone.R R/utils.R R/vizGenes.R README.md
_pkgdown.yml
data/contig_list.rda
data/mini_contig_list.rda
data/scRep_example.rda
index.md
inst/CITATION
inst/WORDLIST
inst/pkgdown.yml
man/StartracDiversity.Rd man/addVariable.Rd man/alluvialClones.Rd man/clonalAbundance.Rd man/clonalBias.Rd man/clonalCluster.Rd man/clonalCompare.Rd man/clonalDiversity.Rd man/clonalHomeostasis.Rd man/clonalLength.Rd man/clonalNetwork.Rd man/clonalOccupy.Rd man/clonalOverlap.Rd man/clonalOverlay.Rd man/clonalProportion.Rd man/clonalQuant.Rd man/clonalRarefaction.Rd man/clonalScatter.Rd man/clonalSizeDistribution.Rd man/combineBCR.Rd man/combineExpression.Rd man/combineTCR.Rd man/contig_list.Rd man/createHTOContigList.Rd man/exportClones.Rd
man/figures/screpertoire_hex.png
man/getCirclize.Rd man/highlightClones.Rd man/loadContigs.Rd man/mini_contig_list.Rd man/percentAA.Rd man/percentGenes.Rd man/percentKmer.Rd man/percentVJ.Rd man/positionalEntropy.Rd man/positionalProperty.Rd man/scRep_example.Rd man/scRepertoire-package.Rd man/subsetClones.Rd man/vizGenes.Rd
scRepertoire.Rproj
src/.gitignore
src/RcppExports.cpp
src/aaKmers.cpp
src/constructConDfAndParseBCR.cpp
src/constructConDfAndparseTCR.cpp
src/ntKmers.cpp
src/scRepHelper.h
tests/spelling.R tests/testthat.R
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tests/testthat/_snaps/clonalHomeostasis/clonalhomeostasis-plot.svg
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tests/testthat/_snaps/clonalLength/clonallength-trb-plot.svg
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tests/testthat/_snaps/clonalOverlap/clonaloverlap-cosine-plot.svg
tests/testthat/_snaps/clonalOverlap/clonaloverlap-coverlap-plot.svg
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tests/testthat/_snaps/clonalOverlap/clonaloverlap-raw-plot.svg
tests/testthat/_snaps/clonalOverlap/clonaloverlap-reorder-plot.svg
tests/testthat/_snaps/clonalOverlay/clonaloverlay-clonalproportion-plot.svg
tests/testthat/_snaps/clonalOverlay/clonaloverlay-plot.svg
tests/testthat/_snaps/clonalProportion/clonalproportion-plot.svg
tests/testthat/_snaps/clonalQuant/clonalquant-scaled-plot.svg
tests/testthat/_snaps/clonalQuant/clonalquant-unscaled-plot.svg
tests/testthat/_snaps/clonalRarefaction/clonalclonalrarefaction-h0-p1-plot.svg
tests/testthat/_snaps/clonalRarefaction/clonalclonalrarefaction-h1-p2-plot.svg
tests/testthat/_snaps/clonalRarefaction/clonalclonalrarefaction-h2-p3-plot.svg
tests/testthat/_snaps/clonalScatter/clonalscatter-proportion-plot.svg
tests/testthat/_snaps/clonalScatter/clonalscatter-raw-plot.svg
tests/testthat/_snaps/clonalSizeDistribution/clonalsizedistribution-plot.svg
tests/testthat/_snaps/percentAA/percentaa-plot.svg
tests/testthat/_snaps/percentGenes/percentgenes-plot.svg
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tests/testthat/_snaps/positionalEntropy/positionalentropy-trb-plot.svg
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tests/testthat/testdata/clustering/clonalCluster_TRBaa_data.rds
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tests/testthat/testdata/combineContigs/combineTCR_list_removeNA.rds
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tests/testthat/testdata/load/loadContigs_Parse.rds
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tests/testthat/testdata/processing/subsetClones_data.rds
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tests/testthat/testdata/seuratFunctions/alluvialClones_exportTable.rds
tests/testthat/testdata/seuratFunctions/clonalBias_exportTable.rds
tests/testthat/testdata/seuratFunctions/clonalNetwork_exportClones.rds
tests/testthat/testdata/seuratFunctions/clonalNetwork_exportTable.rds
tests/testthat/testdata/seuratFunctions/clonalOccupy_exportTable.rds
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tests/testthat/testdata/seuratFunctions/getCirclize_default_output.rds
tests/testthat/testdata/seuratFunctions/getCirclize_proportion_output.rds
tests/testthat/testdata/seuratFunctions/highlightClones_meta.rds
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tests/testthat/testdata/utils/bound.input.return_data.rds
tests/testthat/testdata/utils/checkContigs_data.rds
tests/testthat/testdata/utils/constructConDfAndParseTCRInput.rds
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tests/testthat/testdata/utils/expected_con_df.rds
tests/testthat/testdata/utils/expression2List_by.orig.ident_data.rds
tests/testthat/testdata/utils/expression2List_data.rds
tests/testthat/testdata/utils/filteringNA_metadata.rds
tests/testthat/testdata/utils/get.coord_data.rds
tests/testthat/testdata/utils/grabMeta_data.rds
tests/testthat/testdata/utils/list.input.return_data.rds
tests/testthat/testdata/utils/makeGenes_T_expected.rds
tests/testthat/testdata/utils/makeGenes_T_input.rds
tests/testthat/testdata/utils/parseTCR_result.rds
tests/testthat/testdata/utils/removingMulti_data.rds
tests/testthat/testdata/visualizations/clonalDiversity_exportTable.rds
tests/testthat/testdata/visualizations/clonalHomeostasis_exportTable.rds
tests/testthat/testdata/visualizations/clonalProportion_exportTable.rds
tests/testthat/testdata/visualizations/clonalRarefaction_h0_p1_exportTable.rds
tests/testthat/testdata/visualizations/clonalRarefaction_h1_p2_exportTable.rds
tests/testthat/testdata/visualizations/clonalRarefaction_h2_p3_exportTable.rds
tests/testthat/testdata/visualizations/clonalScatter_exportTable.rds
tests/testthat/testdata/visualizations/clonalSizeDistribution_exportTable.rds
tests/testthat/testdata/visualizations/percentAA_exportTable.rds
tests/testthat/testdata/visualizations/percentGenes_exportTable.rds
tests/testthat/testdata/visualizations/percentVJ_exportTable.rds
vignettes/articles/Attaching_SC.Rmd vignettes/articles/Clonal_Bias.Rmd vignettes/articles/Clonal_Cluster.Rmd vignettes/articles/Clonal_Diversity.Rmd vignettes/articles/Clonal_Dynamics.Rmd vignettes/articles/Clonal_Visualizations.Rmd vignettes/articles/Combining_Contigs.Rmd vignettes/articles/FAQ.Rmd vignettes/articles/Ibex.Rmd vignettes/articles/Installation.Rmd vignettes/articles/Loading.Rmd vignettes/articles/Processing.Rmd vignettes/articles/Repertoire_Summary.Rmd vignettes/articles/Running_Escape.Rmd vignettes/articles/SC_Visualizations.Rmd vignettes/articles/Trex.Rmd vignettes/vignette.Rmd
ncborcherding/scRepertoire documentation built on May 8, 2024, 6:28 a.m.

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