Files in qingjian1991/MPTevol
Clonal Evolutionary History and Metastatic Routines Analysis for Multiple Primary Tumors
.Rbuildignore
.github/.gitignore
.gitignore
DESCRIPTION
LICENSE.md
MPTevol.Rproj
Makefile
NAMESPACE
NEWS.md
R/MPTevol-package.R
R/auxiliary.R
R/calKaKs.R
R/calPropDriver.R
R/calRoutines.R
R/classS4.R
R/getClinSites.R
R/inferClonalTrees.R
R/maf2variants.R
R/plotCNA.R
R/plotCNAProfile.R
R/plotCNATree.R
R/plotMutTree.R
R/plotVafCluster.R
R/readCNAProfile.R
R/readMaf.R
R/readSegment.R
R/splitSegment.R
R/tree2timescape.R
R/utils-pipe.R
R/validation.R
R/viewTrees.R
README.Rmd
README.md
Test.R
_pkgdown.yml
data/submod_13r_3w.rda
data/variants.rda
data/variants.ref.rda
docs/404.html
docs/LICENSE.html
docs/authors.html
docs/deps/bootstrap-5.1.0/bootstrap.bundle.min.js
docs/deps/bootstrap-5.1.0/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.1.0/bootstrap.min.css
docs/deps/data-deps.txt
docs/deps/jquery-3.6.0/jquery-3.6.0.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.map
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/MPTevol-package.html
docs/reference/Seg-class.html
docs/reference/calKaKs.html
docs/reference/calRoutines.html
docs/reference/figures/MPTevol.jpg
docs/reference/figures/MPTevol_Structure.jpg
docs/reference/getClinSites.html
docs/reference/getKaKs.html
docs/reference/index.html
docs/reference/inferClonalTrees.html
docs/reference/pipe.html
docs/reference/plotCNAProfile.html
docs/reference/plotCNAtree.html
docs/reference/plotMutTree.html
docs/reference/plotVafCluster.html
docs/reference/readCNAProfile.html
docs/reference/set.colors.html
docs/reference/splitSegment.html
docs/reference/tree2timescape.html
docs/reference/viewTrees.html
docs/reference/write.fasta.html
docs/search.json
docs/sitemap.xml
documents/MPTevol.Rmd
inst/extdata/IntOGen-Drivers-Cancer_Genes.tsv
inst/extdata/meskit.sequenza.CNAs.txt
inst/extdata/meskit.split.CCF.txt
inst/extdata/meskit.split.clinical.txt
inst/extdata/meskit.split.mutation.txt
inst/extdata/meskit.split1.CCF.txt
inst/extdata/meskit.split1.clinical.txt
inst/extdata/meskit.split1.mutation.txt
inst/extdata/oncokb_biomarker_drug_associations.tsv
inst/extdata/tree_final.dist
man/MPTevol-package.Rd
man/Seg-class.Rd
man/calKaKs.Rd
man/calPropDriver.Rd
man/calRoutines.Rd
man/figures/MPTevol.jpg
man/figures/MPTevol_Structure.jpg
man/getClinSites.Rd
man/getKaKs.Rd
man/inferClonalTrees.Rd
man/maf2variants.Rd
man/pipe.Rd
man/plotCNA.Rd
man/plotCNAProfile.Rd
man/plotCNAtree.Rd
man/plotMutTree.Rd
man/plotVafCluster.Rd
man/readCNAProfile.Rd
man/readMaf.Rd
man/set.colors.Rd
man/splitSegment.Rd
man/tree2timescape.Rd
man/viewTrees.Rd
man/write.fasta.Rd
vignettes/.gitignore
vignettes/MPTevol.Rmd
