Files in wuaipinglab/sitePath
Phylogenetic pathway–dependent recognition of fixed substitutions and parallel mutations

.Rbuildignore
.github/.gitignore
.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/RcppExports.R R/SNPsites.R R/addMSA.R R/allSitesName.R R/as.data.frame.R R/extractSite.R R/extractTips.R R/fixationIndels.R R/fixationPath.R R/fixationSites.R R/groupTips.R R/lineagePath.R R/paraFixSites.R R/parallelSites.R R/plotFunctions.R R/plotMutSites.R R/plotSingleSite.R R/printFunctions.R R/reexports.R R/siteNumbering.R R/sitePath-deprecated.R R/sitesMinEntropy.R R/staticData.R README.Rmd README.md
data/h3n2_align.rda
data/h3n2_align_reduced.rda
data/h3n2_tree.rda
data/h3n2_tree_reduced.rda
data/sars2_align.rda
data/sars2_tree.rda
data/zikv_align.rda
data/zikv_align_reduced.rda
data/zikv_tree.rda
data/zikv_tree_reduced.rda
inst/extdata/WNV.newick
inst/extdata/ZIKV.fasta
inst/extdata/ZIKV.newick
man/SNPsites.Rd man/addMSA.Rd man/allSitesName.Rd man/as.data.frame.Rd man/extractSite.Rd man/extractTips.Rd man/fixationIndels.Rd man/fixationPath.Rd man/fixationSites.Rd man/groupTips.Rd man/h3n2_align.Rd man/h3n2_tree.Rd man/lineagePath.Rd man/paraFixSites.Rd man/parallelSites.Rd man/plotFunctions.Rd man/plotMutSites.Rd man/plotSingleSite.Rd man/reexports.Rd man/sars2_align.Rd man/sars2_tree.Rd man/setSiteNumbering.Rd man/similarityMatrix.Rd man/sitePath-deprecated.Rd man/sitesMinEntropy.Rd man/zikv_align.Rd man/zikv_tree.Rd
src/.gitignore
src/RcppExports.cpp
src/lumpyCluster.cpp
src/lumpyCluster.h
src/minEntropy.cpp
src/minEntropy.h
src/searchNode.cpp
src/searchTree.cpp
src/treemer.cpp
src/treemer.h
src/util.cpp
tests/testthat.R tests/testthat/test-SNPsites.R tests/testthat/test-addMSA.R tests/testthat/test-allSitesName.R tests/testthat/test-as.data.frame.R tests/testthat/test-fixationPath.R tests/testthat/test-fixationSites.R tests/testthat/test-groupTips.R tests/testthat/test-lineagePath.R tests/testthat/test-multiprocessing.R tests/testthat/test-paraFixSites.R tests/testthat/test-parallelSites.R tests/testthat/test-plotFunctions.R tests/testthat/test-plotSingleSite.R tests/testthat/test-printFunctions.R tests/testthat/test-reexports.R tests/testthat/test-similarityMatrix.R tests/testthat/test-siteNumbering.R tests/testthat/test-sitesMinEntropy.R vignettes/sitePath.Rmd
wuaipinglab/sitePath documentation built on July 25, 2021, 9:11 p.m.