Files in Fraternalilab/BrepPhylo
BrepPhylo: R package for phylogenetic analysis of B cell repertoire
BrepPhylo.Rproj
BrepPhylo_logo.png
DESCRIPTION
LICENSE
NAMESPACE
R/CSR.R
R/IgPhyML.R
R/alignmentValidCodons.R
R/cloneArborescence.R
R/cloneLineage.R
R/data.R
R/doBatchCloneAnalysis.R
R/germlineDistances.R
R/getArborescence.R
R/getDistancesFromTree.R
R/is.valid.IsotypeSwitch.R
R/makeAlignmentPDF.R
R/msaPrettyPrint_extended.R
R/support.R
R/zzz.R
README.md
data/Vgermline.R
data/Vgermline.rda
data/Vgermline_gapped.R
data/Vgermline_gapped.rda
inst/exe/dnapars
inst/extdata/CV233_batch_analysis.rds
inst/extdata/CV325_batch_analysis.rds
inst/extdata/clone_188.csv
inst/extdata/clone_188.tree
inst/extdata/input.csv
inst/extdata/input_GermlineDistances.csv
inst/python/edmond_arborescence.py
man/GermlineLikeness.Rd
man/IgPhyML.Rd
man/Vgermline.Rd
man/Vgermline_gapped.Rd
man/addCloneToCompleted.Rd
man/alignmentValidCodons.Rd
man/cloneArborescence.Rd
man/cloneLineage.Rd
man/convertDNAStringSetToList.Rd
man/curDateTime.Rd
man/doBatchCloneAnalysis.Rd
man/getArborescence.Rd
man/getCSEvents.Rd
man/getColourVectorFromLevels.Rd
man/getDistPercentile.Rd
man/getDistancesFromTree.Rd
man/getGermlineDistance.Rd
man/getGermlineLikeness.Rd
man/getSummaryFromBatch.Rd
man/is.valid.IsotypeSwitch.Rd
man/makeAlignmentPDF.Rd
man/msaPrettyPrint_extended.Rd
man/plotCSRsummary.Rd
man/summariseCSR.Rd
man/summariseGermlineDistance.Rd
tests/testthat.R
tests/testthat/test-clonearborescence.R
tests/testthat/test-clonelineage.R
vignettes/.gitignore
vignettes/bibliography.bib
vignettes/figures/phylogenetic/cloneLineage_benchmark.png
vignettes/figures/phylogenetic/clone_1548_part_1.png
vignettes/figures/phylogenetic/clone_188_part_1.png
vignettes/figures/phylogenetic/input/cloneLineage_benchmark.pdf
vignettes/nar-webserver-issue.csl
vignettes/phylogenetic.Rmd
vignettes/phylogenetic.html
vignettes/phylogenetic.pdf
