Files in szhaolab/diffdriver
Identify differential selection
.gitignore
DESCRIPTION
NAMESPACE
R/comparators.R
R/ddmodel.R
R/ddmodel_nl.R
R/diffdriver.R
R/diffdriver_prepdata.R
R/drivermaps_loglik.R
R/drivermaps_readdata.R
R/matrixlistToBMR.R
R/mut2hotspot.R
R/plots.R
R/sysdata.rda
README.md
_pkgdown.yml
before_package/countLRT.R
before_package/run_simulate2_onegene.R
before_package/run_simulate_onegene.R
before_package/run_simulate_onegene_2019-05-06.R
before_package/run_simulate_onegene_2019-05-12.R
before_package/run_simulate_onegene_2019-05-21.R
before_package/test.R
data-raw/Prep_default.R
data-raw/Prep_example.R
data-raw/to_clean/OG.txt
data-raw/to_clean/Prep_200genes_data.R
data-raw/to_clean/TSG.txt
data-raw/to_clean/codeSignature.Rd
data-raw/to_clean/codesig.Rd
data-raw/to_clean/colmu_sd_funct78.Rdata
data-raw/to_clean/ff.Rd
data-raw/to_clean/genename200.txt
data-raw/to_clean/genenames_OG.txt
data-raw/to_clean/genenames_TSG.txt
data-raw/to_clean/generate_hotspot_seq.R
data-raw/to_clean/hmmOGpar_ASHmean.rds
data-raw/to_clean/hotspotsig.R
data-raw/to_clean/ll.Rd
data-raw/to_clean/mappingcode.Rd
data-raw/to_clean/modelmatrix.R
data-raw/to_clean/modelmatrix200.R
data-raw/to_clean/mutp.R
data-raw/to_clean/nttypeNumber.Rd
data-raw/to_clean/parm.R
data-raw/to_clean/parmASHmean.Rdata
data-raw/to_clean/run_simulation.R
data-raw/to_clean/sgdata.R
data-raw/to_clean/signatures.Rd
data-raw/to_clean/simuPara1.R
data-raw/to_clean/simuParameters.R
data/to_clean/BMR.rda
data/to_clean/BMRlist.rda
data/to_clean/Fe.rda
data/to_clean/Fpars.rda
data/to_clean/N.rda
data/to_clean/README
data/to_clean/beta_og.Rd
data/to_clean/beta_tp53.Rd
data/to_clean/beta_tsg.Rd
data/to_clean/codeSignature.rda
data/to_clean/ff.rda
data/to_clean/genename200.rda
data/to_clean/hmmcoeff.rda
data/to_clean/hotseq.rda
data/to_clean/hotseq0.rda
data/to_clean/hotseq1.rda
data/to_clean/hotseq2.rda
data/to_clean/hotseq3.rda
data/to_clean/hotseq6.rda
data/to_clean/hotspot1sig.rda
data/to_clean/hotspot2sig.rda
data/to_clean/ll.rda
data/to_clean/og.rda
data/to_clean/ogParm.rda
data/to_clean/parmASHmean.rda
data/to_clean/sganno.rda
data/to_clean/sgdata.rda
data/to_clean/sgmatrix.rda
data/to_clean/sig.rda
data/to_clean/signatures.rda
data/to_clean/testdataBinary.rda
data/to_clean/testdataCont.rda
data/to_clean/tsgParm.rda
diffdriver.Rproj
docs/404.html
docs/articles/diffdriver_tutorial.html
docs/articles/diffdriver_tutorial_files/figure-html/plot-1.png
docs/articles/index.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/ddmcode.html
docs/reference/ddmodel.html
docs/reference/ddmodel_binary.html
docs/reference/ddmodel_binary_simple.html
docs/reference/diffdriver.html
docs/reference/genebinom.html
docs/reference/genefisher.html
docs/reference/genelr.html
docs/reference/index.html
docs/reference/mlr.html
docs/reference/mlr.v2.html
docs/reference/optifix.html
docs/reference/plot_mut.html
docs/sitemap.xml
inst/extdata/OG.txt
inst/extdata/TSG.txt
inst/extdata/colmu_sd_funct78.Rdata
inst/extdata/example_gene.txt
inst/extdata/example_mutations.txt
inst/extdata/example_phenotypes.txt
inst/extdata/hmmOGpar_ASHmean.rds
inst/extdata/parmASHmean.Rdata
man/ddmcode.Rd
man/ddmodel.Rd
man/ddmodel_binary.Rd
man/ddmodel_binary_simple.Rd
man/diffdriver.Rd
man/genebinom.Rd
man/genefisher.Rd
man/genelr.Rd
man/mlr.Rd
man/mlr.v2.Rd
man/optifix.Rd
man/plot_mut.Rd
scripts/bmr_signature.R
scripts/hotspot.R
scripts/simulate_functions.R
tests/testthat.R
tests/testthat/test-simulate_binary.R
tests/testthat/test.R
vignettes/diffdriver_tutorial.Rmd
