LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors
Version 1.4.0

This R package analyzes high-throughput sequencing of T and B cell receptor complementarity determining region 3 (CDR3) sequences generated by Adaptive Biotechnologies' ImmunoSEQ assay. Its input comes from tab-separated value (.tsv) files exported from the ImmunoSEQ analyzer.

AuthorDavid Coffey <dcoffey@fredhutch.org>
Bioconductor views Alignment MultipleSequenceAlignment Sequencing Software TargetedResequencing Technology
Date of publicationNone
MaintainerDavid Coffey <dcoffey@fredhutch.org>
LicenseArtistic-2.0
Version1.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("LymphoSeq")

Getting started

README.md
Analysis of high-throughput sequencing of T and B cell receptors with LymphoSeq

Popular man pages

alignSeq: Align mutliple sequences
chordDiagramVDJ: Chord diagram of VJ or DJ gene associations
commonSeqsBar: Common sequences bar plot
differentialAbundance: Differential abundance analysis
seqMatrix: Sequence matrix
similarityMatrix: Similarity score matrix
topFreq: Top frequencies
See all...

All man pages Function index File listing

Man pages

alignSeq: Align mutliple sequences
bhattacharyyaCoefficient: Bhattacharyya coefficient
bhattacharyyaMatrix: Bhattacharyya matrix
chordDiagramVDJ: Chord diagram of VJ or DJ gene associations
clonality: Clonality
clonalRelatedness: Clonal relatedness
cloneTrack: Clone tracking plot
commonSeqs: Common sequences in two or more samples
commonSeqsBar: Common sequences bar plot
commonSeqsPlot: Common sequences plot
commonSeqsVenn: Common sequences Venn diagram
differentialAbundance: Differential abundance analysis
exportFasta: Export sequences in fasta format
geneFreq: Gene frequencies
lorenzCurve: Lorenz curve
mergeFiles: Merge files
pairwisePlot: Pairwise comparison plot
phyloTree: Create phylogenetic tree
productive: Productive sequences
productiveSeq: Productive sequences
readImmunoSeq: Read ImmunoSeq files
removeSeq: Remove sequence
searchPublished: Search for T cell receptor beta CDR3 amino acid sequences...
searchSeq: Search for a sequence
seqMatrix: Sequence matrix
similarityMatrix: Similarity score matrix
similarityScore: Similarity score
topFreq: Top frequencies
topSeqs: Top sequences
topSeqsPlot: Cumulative frequency bar plot of top sequences
uniqueSeqs: Unique sequences

Functions

alignSeq Man page Source code
bhattacharyyaCoefficient Man page Source code
bhattacharyyaMatrix Man page Source code
chordDiagramVDJ Man page Source code
clonalRelatedness Man page Source code
clonality Man page Source code
cloneTrack Man page Source code
commonSeqs Man page Source code
commonSeqsBar Man page Source code
commonSeqsPlot Man page Source code
commonSeqsVenn Man page Source code
differentialAbundance Man page Source code
exportFasta Man page Source code
geneFreq Man page Source code
lorenzCurve Man page Source code
mergeFiles Man page Source code
pairwisePlot Man page Source code
phyloTree Man page Source code
productive Man page Source code
productiveSeq Man page Source code
readImmunoSeq Man page Source code
removeSeq Man page Source code
searchPublished Man page Source code
searchSeq Man page Source code
seqMatrix Man page Source code
similarityMatrix Man page Source code
similarityScore Man page Source code
topFreq Man page Source code
topSeqs Man page Source code
topSeqsPlot Man page Source code
uniqueSeqs Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/alignSeq.R
R/bhattacharyyaCoefficient.R
R/bhattacharyyaMatrix.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/differentialAbundance.R
R/exportFasta.R
R/geneFreq.R
R/lorenzCurve.R
R/mergeFiles.R
R/pairwisePlot.R
R/phyloTree.R
R/productive.R
R/productiveSeq.R
R/readImmunoSeq.R
R/removeSeq.R
R/searchPublished.R
R/searchSeq.R
R/seqMatrix.R
R/similarityMatrix.R
R/similarityScore.R
R/topFreq.R
R/topSeqs.R
R/topSeqsPlot.R
R/uniqueSeqs.R
README.md
build
build/vignette.rds
inst
inst/NEWS
inst/doc
inst/doc/LymphoSeq.R
inst/doc/LymphoSeq.Rmd
inst/doc/LymphoSeq.html
inst/extdata
inst/extdata/IGH_metadata.csv
inst/extdata/IGH_sequencing
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_metadata.csv
inst/extdata/TCRB_sequencing
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
man/alignSeq.Rd
man/bhattacharyyaCoefficient.Rd
man/bhattacharyyaMatrix.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/differentialAbundance.Rd
man/exportFasta.Rd
man/geneFreq.Rd
man/lorenzCurve.Rd
man/mergeFiles.Rd
man/pairwisePlot.Rd
man/phyloTree.Rd
man/productive.Rd
man/productiveSeq.Rd
man/readImmunoSeq.Rd
man/removeSeq.Rd
man/searchPublished.Rd
man/searchSeq.Rd
man/seqMatrix.Rd
man/similarityMatrix.Rd
man/similarityScore.Rd
man/topFreq.Rd
man/topSeqs.Rd
man/topSeqsPlot.Rd
man/uniqueSeqs.Rd
vignettes
vignettes/LymphoSeq.Rmd
LymphoSeq documentation built on May 20, 2017, 9:42 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.