Files in elulu3/LymphoSeqTest
Analyze high-throughput sequencing of T and B cell receptors
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.gitignore
DESCRIPTION
NAMESPACE
R/alignSeq.R
R/chordDiagramVDJ.R
R/clonalRelatedness.R
R/clonality.R
R/cloneTrack.R
R/commonSeqs.R
R/commonSeqsBar.R
R/commonSeqsPlot.R
R/commonSeqsVenn.R
R/countKmer.R
R/differentialAbundance.R
R/exportFasta.R
R/geneFreq.R
R/getLorenz.R
R/phyloTree.R
R/plotAlignment.R
R/plotLorenzCurve.R
R/plotPairwise.R
R/plotTrack.R
R/plotTrackSingular.R
R/rarefactionCurve.R
R/readGliphTable.R
R/readImmunoSeq.R
R/readProductiveSeq.R
R/removeSeq.R
R/runINext.R
R/scoringMatrix.R
R/searchDB.R
R/searchPublished.R
R/searchSeq.R
R/seqMatrix.R
R/topFreq.R
R/topSeqs.R
R/topSeqsPlot.R
R/uniqueSeqs.R
README.Rmd
README.md
_pkgdown.yml
data/prevalenceTRB.rda
data/publishedTRB.rda
inst/extdata/AIRR_fields.csv
inst/extdata/IGH_metadata.csv
inst/extdata/IGH_sequencing/IGH_MVQ108911A_BL.tsv
inst/extdata/IGH_sequencing/IGH_MVQ194745A_BL.tsv
inst/extdata/IGH_sequencing/IGH_MVQ81231A_BL.tsv
inst/extdata/IGH_sequencing/IGH_MVQ89037A_BL.tsv
inst/extdata/IGH_sequencing/IGH_MVQ90143A_BL.tsv
inst/extdata/IGH_sequencing/IGH_MVQ92552A_BL.tsv
inst/extdata/IGH_sequencing/IGH_MVQ93505A_BL.tsv
inst/extdata/IGH_sequencing/IGH_MVQ93631A_BL.tsv
inst/extdata/IGH_sequencing/IGH_MVQ94865A_BL.tsv
inst/extdata/IGH_sequencing/IGH_MVQ95413A_BL.tsv
inst/extdata/TCRB_gliph/015V04005438_CFAR.tsv
inst/extdata/TCRB_gliph/015V05003835_CFAR.tsv
inst/extdata/TCRB_gliph/015V05004637_CFAR.tsv
inst/extdata/TCRB_gliph/015V05005267_CFAR.tsv
inst/extdata/TCRB_metadata.csv
inst/extdata/TCRB_sequencing/TRB_CD4_949.tsv
inst/extdata/TCRB_sequencing/TRB_CD8_949.tsv
inst/extdata/TCRB_sequencing/TRB_CD8_CMV_369.tsv
inst/extdata/TCRB_sequencing/TRB_Unsorted_0.tsv
inst/extdata/TCRB_sequencing/TRB_Unsorted_1320.tsv
inst/extdata/TCRB_sequencing/TRB_Unsorted_1496.tsv
inst/extdata/TCRB_sequencing/TRB_Unsorted_32.tsv
inst/extdata/TCRB_sequencing/TRB_Unsorted_369.tsv
inst/extdata/TCRB_sequencing/TRB_Unsorted_83.tsv
inst/extdata/TCRB_sequencing/TRB_Unsorted_949.tsv
man/aggreateSeq.Rd
man/alignSeq.Rd
man/bhattacharyyaCoefficient.Rd
man/chordDiagramVDJ.Rd
man/clonalRelatedness.Rd
man/clonality.Rd
man/cloneTrack.Rd
man/commonSeqs.Rd
man/commonSeqsBar.Rd
man/commonSeqsPlot.Rd
man/commonSeqsVenn.Rd
man/countKmer.Rd
man/differentialAbundance.Rd
man/exportFasta.Rd
man/geneFreq.Rd
man/getGliphTable.Rd
man/getLorenz.Rd
man/getRelatedness.Rd
man/lorenzCurve.Rd
man/pairwisePlot.Rd
man/percentSI.Rd
man/phyloTree.Rd
man/plotAlignment.Rd
man/plotRarefactionCurve.Rd
man/plotTrack.Rd
man/plotTrackSingular.Rd
man/productiveSeq.Rd
man/readGliph.Rd
man/readImmunoSeq.Rd
man/removeSeq.Rd
man/runINext.Rd
man/scoringMatrix.Rd
man/searchDB.Rd
man/searchIreceptor.Rd
man/searchPublished.Rd
man/searchSeq.Rd
man/seqMatrix.Rd
man/similarityScore.Rd
man/sorensenIndex.Rd
man/summarySeq.Rd
man/topFreq.Rd
man/topSeqs.Rd
man/topSeqsPlot.Rd
man/uniqueSeqs.Rd
tests/testthat.R
tests/testthat/test_align.R
tests/testthat/test_clonality.R
tests/testthat/test_clonalrelatedness.R
tests/testthat/test_countkmer.R
tests/testthat/test_data/015V06013979_CFAR.tsv
tests/testthat/test_data/015V12001549_CFAR.tsv
tests/testthat/test_data/015V12001685_CFAR_R.tsv
tests/testthat/test_data/015V12003105_CFAR.tsv
tests/testthat/test_data/gliph/015V04005438_CFAR.tsv
tests/testthat/test_data/gliph/015V05003835_CFAR.tsv
tests/testthat/test_data/prevalenceTRB.rda
tests/testthat/test_genefreq.R
tests/testthat/test_gliph.R
tests/testthat/test_prodseq.R
tests/testthat/test_reader.R
tests/testthat/test_searchseq.R
tests/testthat/test_topseq.R
