Name Mode Size
..
alignSeq.Rd 100644 3 kb
bhattacharyyaCoefficient.Rd 100644 1 kb
bhattacharyyaMatrix.Rd 100644 1 kb
chordDiagramVDJ.Rd 100644 2 kb
clonalRelatedness.Rd 100644 2 kb
clonality.Rd 100644 2 kb
cloneTrack.Rd 100644 4 kb
commonSeqs.Rd 100644 1 kb
commonSeqsBar.Rd 100644 2 kb
commonSeqsPlot.Rd 100644 2 kb
commonSeqsVenn.Rd 100644 1 kb
differentialAbundance.Rd 100644 2 kb
exportFasta.Rd 100644 1 kb
geneFreq.Rd 100644 2 kb
lorenzCurve.Rd 100644 2 kb
mergeFiles.Rd 100644 1 kb
pairwisePlot.Rd 100644 2 kb
phyloTree.Rd 100644 2 kb
productive.Rd 100644 2 kb
productiveSeq.Rd 100644 2 kb
readImmunoSeq.Rd 100644 4 kb
removeSeq.Rd 100644 1 kb
searchPublished.Rd 100644 1 kb
searchSeq.Rd 100644 3 kb
seqMatrix.Rd 100644 2 kb
similarityMatrix.Rd 100644 1 kb
similarityScore.Rd 100644 1 kb
topFreq.Rd 100644 2 kb
topSeqs.Rd 100644 1 kb
topSeqsPlot.Rd 100644 1 kb
uniqueSeqs.Rd 100644 1 kb
README.md
# LymphoSeq 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](http://www.adaptivebiotech.com/immunoseq). ### Installation instructions #### Install release version 1.4 ###### Install from [Bioconductor](https://www.bioconductor.org/packages/LymphoSeq) ``` source("https://bioconductor.org/biocLite.R") biocLite("LymphoSeq") ``` #### Install developer version 1.5 ###### Option 1: Install from [Bioconductor developer branch](https://www.bioconductor.org/developers/how-to/useDevel/) ``` # Switch to Bioconductor developer branch (requires latest version of R) library(BiocInstaller) useDevel() # Download developer release source("https://bioconductor.org/biocLite.R") biocLite("LymphoSeq") # Switch back to Bioconductor release branch library(BiocInstaller) useDevel() ``` ###### Option 2: Install from GitHub ``` # Install the latest version of Bioconductor source("https://bioconductor.org/biocLite.R") biocLite() # Download developer tools install.packages("devtools") # Download package from GitHub devtools::install_github("davidcoffey/LymphoSeqDB") devtools::install_github("davidcoffey/LymphoSeq") ``` ### Documentation * [LymphoSeq vignette](http://bioconductor.org/packages/release/bioc/vignettes/LymphoSeq/inst/doc/LymphoSeq.html) * [LymphoSeq manual](https://bioconductor.org/packages/release/bioc/manuals/LymphoSeq/man/LymphoSeq.pdf) * [LymphoSeq news](https://bioconductor.org/packages/release/bioc/news/LymphoSeq/NEWS) ### Citation Coffey D (2017). LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors. R package version 1.4.