steverozen/mSigHdp
Mutational signature discovery using HDP (hierarchical Dirichlet process)

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Mutational signature discovery using HDP (hierarchical Dirichlet process)

.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.gitignore
DESCRIPTION
LICENSE.md
NAMESPACE
NEWS.md R/Burnin.R R/CleanChlist.R R/CombineChainsAndExtractSigs.R R/ComponentDiagnosticPlotting.R R/ExtendBurnin.R R/GenerateAverageCluster.R R/GeneratePriorppindex.R R/Generateppindex.R R/GetInputCatalogAsMatrix.R R/GetPossibleICAMSCatalog.R R/GibbsSamplingAfterBurnin.R R/ParallelGibbsSample.R R/PlotSamplesHighSigExp.R R/PrepInit.R R/RunHdpxParallel.R R/SaveAnalysis.R R/SetupAndActivate.R R/SetupAndPosterior.R R/downsample.R R/show_downsample_curves.R README.md
data-raw/Hierarchical.dirichlet.process.for.mutational.signatures.docx
data-raw/container_scripts/container_build_command.txt
data-raw/container_scripts/mSigHdp_container_installation.pdf
data-raw/container_scripts/msighdp.def
data-raw/container_scripts/test_catalog.csv
data-raw/container_scripts/test_mSigHdp.R data-raw/old.code.and.notes/ActivateAndBurnin2.R data-raw/old.code.and.notes/CopyOfCombinePosteriorChains.R data-raw/old.code.and.notes/CopyOfPlotSamplesHighSigExp.R data-raw/old.code.and.notes/ExtendIterationAndPosterior.R data-raw/old.code.and.notes/NaN.example.RunHdpxParallel.example.R data-raw/old.code.and.notes/OldRunHdpParallel.R data-raw/old.code.and.notes/ParallelPosteriorafterBurnin.R data-raw/old.code.and.notes/PriorSetupAndActivate.R data-raw/old.code.and.notes/RunHdpxParallel.example.R data-raw/old.code.and.notes/SetupAndPosterior2.R data-raw/old.code.and.notes/code.to.include/mSigTools.v0.13.R data-raw/old.code.and.notes/code.using.nicola.roberts.hdp/CombinePosteriorChains.R data-raw/old.code.and.notes/code.using.nicola.roberts.hdp/RunAndEvalHdp5.R data-raw/old.code.and.notes/code.using.nicola.roberts.hdp/Runhdp5.R data-raw/old.code.and.notes/code.using.nicola.roberts.hdp/RunhdpInternal5.R data-raw/old.code.and.notes/continue.burnin.script.R data-raw/old.code.and.notes/data.R data-raw/old.code.and.notes/downsample.Rmd
data-raw/old.code.and.notes/downsample.html
data-raw/old.code.and.notes/example.plot.exposure.to.pdf.R data-raw/old.code.and.notes/example.scripts/WES.id.R data-raw/old.code.and.notes/example.scripts/s5.R data-raw/old.code.and.notes/example.scripts/x.R data-raw/old.code.and.notes/example.scripts/x5K25.R data-raw/old.code.and.notes/example.scripts/x5K25b10000n2000.R data-raw/old.code.and.notes/example.scripts/x5K25b2000n2000.R data-raw/old.code.and.notes/example.scripts/y5K25b10000n2000.R data-raw/old.code.and.notes/example.scripts/z4K25b10000n2000.R data-raw/old.code.and.notes/example.scripts/zz4K25b40000n2000.R data-raw/old.code.and.notes/parallel-initial-burnin-script.R data-raw/old.code.and.notes/posterior.sample.after.burnin.script.R data-raw/old.code.and.notes/previous-exposure-code/NewPlotExposure.R data-raw/old.code.and.notes/previous-exposure-code/PlotExposure.R data-raw/old.code.and.notes/previous-exposure-code/test-PlotExposure.R
data-raw/old.code.and.notes/profile.c.code.notes.txt
data-raw/old.code.and.notes/small.hdpSampleChain.Rdata
data-raw/old.code.and.notes/source-file/mSigHdp_0.0.0.9026.tar.gz
data-raw/old.code.and.notes/start.burnin.script.R data-raw/old.code.and.notes/test.script.CombinePosteriorChains.R data-raw/old.code.and.notes/tmpPrepInit.R
inst/WORDLIST
mSigHdp.Rproj
mSigHdp.html
mSigHdp_2.1.2.pdf man/Burnin.Rd man/CleanChlist.Rd man/CombineChainsAndExtractSigs.Rd man/ComponentDiagnosticPlotting.Rd man/ExtendBurnin.Rd man/GenerateAverageCluster.Rd man/GeneratePriorppindex.Rd man/Generateppindex.Rd man/GibbsSamplingAfterBurnin.Rd man/ParallelGibbsSample.Rd man/PlotSamplesHighSigExp.Rd man/PrepInit.Rd man/RunHdpxParallel.Rd man/SaveAnalysis.Rd man/SetupAndActivate.Rd man/SetupAndPosterior.Rd man/downsample.Rd man/downsample_spectra.Rd man/show_downsample_curves.Rd
tests/.gitignore
tests/testthat.R
tests/testthat/.gitignore
tests/testthat/RunhdpInternal.testdata/NewRunHdpParallel-fast96-2-cores-downsample.Rdata
tests/testthat/RunhdpInternal.testdata/NewRunHdpParallel-fast96-2-cores-multi-type-T.Rdata
tests/testthat/RunhdpInternal.testdata/NewRunHdpParallel-fast96-2-cores.Rdata
tests/testthat/RunhdpInternal.testdata/RunHdpParallel-fast96-2-cores-multi-type-T.Rdata
tests/testthat/RunhdpInternal.testdata/RunHdpParallel-fast96-2-cores.Rdata
tests/testthat/RunhdpInternal.testdata/RunhdpInternal-fast96-2-cores.Rdata
tests/testthat/RunhdpInternal.testdata/RunhdpInternal-fast96.Rdata
tests/testthat/RunhdpInternal.testdata/mSigHdp.burnin.checkpoint-input.Rdata
tests/testthat/RunhdpInternal.testdata/retval4chains.Rdata
tests/testthat/RunhdpInternal.testdata/t2.out.Rdata
tests/testthat/RunhdpInternal.testdata/test.ActivateAndBurnin.Rdata
tests/testthat/RunhdpInternal.testdata/test.BurninIteration.Rdata
tests/testthat/RunhdpInternal.testdata/test.ChainBurnin.Rdata
tests/testthat/RunhdpInternal.testdata/test.CleanChlist.Rdata
tests/testthat/RunhdpInternal.testdata/test.CombineChainsAndExtractSigs.Rdata
tests/testthat/RunhdpInternal.testdata/test.CombinePosteriorChains.Rdata
tests/testthat/RunhdpInternal.testdata/test.ExtendBurnin.Rdata
tests/testthat/RunhdpInternal.testdata/test.ExtractAfterBurnin.Rdata
tests/testthat/RunhdpInternal.testdata/test.GenerateAverageCluster.Rdata
tests/testthat/RunhdpInternal.testdata/test.Generateppindex.Rdata
tests/testthat/RunhdpInternal.testdata/test.Generateppindex2.Rdata
tests/testthat/RunhdpInternal.testdata/test.Generateppindex3.Rdata
tests/testthat/RunhdpInternal.testdata/test.GibbsSamplingAfterBurnin.Rdata
tests/testthat/RunhdpInternal.testdata/test.MultipleSetupAndPosterior.Rdata
tests/testthat/RunhdpInternal.testdata/test.PrepInit.Rdata
tests/testthat/RunhdpInternal.testdata/test.RunhdpInternal.2.Rdata
tests/testthat/RunhdpInternal.testdata/test.RunhdpInternal3-fast-2-chains.Rdata
tests/testthat/RunhdpInternal.testdata/test.RunhdpInternal4-2types.Rdata
tests/testthat/RunhdpInternal.testdata/test.SetupAndPosterior.Rdata
tests/testthat/SBS96.ground.truth/1.burnin.lik.pdf
tests/testthat/SBS96.ground.truth/1.burnin.output.Rdata
tests/testthat/SBS96.ground.truth/1.type.ground.truth.syn.catalog.csv
tests/testthat/SBS96.ground.truth/2.burnin.lik.pdf
tests/testthat/SBS96.ground.truth/2.burnin.output.Rdata
tests/testthat/SBS96.ground.truth/2.type.ground.truth.syn.catalog.csv
tests/testthat/SBS96.ground.truth/ground.truth.syn.catalog.csv
tests/testthat/SBS96.ground.truth/ground.truth.syn.exposures.csv
tests/testthat/SBS96.ground.truth/ground.truth.syn.sigs.csv
tests/testthat/SBS96.ground.truth/parameters.csv
tests/testthat/SBS96.ground.truth/posterior.sample.chains.output.Rdata
tests/testthat/misc.test.data/1000044.activated.hdp.state.Rdata
tests/testthat/misc.test.data/chlist.Rdata
tests/testthat/tdata/RunHdpParallel-slow-multiF.Rdata
tests/testthat/tdata/RunHdpParallel-slow-multiT.Rdata
tests/testthat/tdata/downsample_spectra_and_result.Rdata
tests/testthat/test-Burnin.R tests/testthat/test-CleanChlist.R tests/testthat/test-CombineChainsAndExtractSigs-fast.R tests/testthat/test-ExtendBurnin.R tests/testthat/test-GenerateAverageCluster.R tests/testthat/test-Generateppindex.R tests/testthat/test-GibbsSamplingAfterBurnin.R tests/testthat/test-ParallelGibbsSample-fast.R tests/testthat/test-PrepInit.R tests/testthat/test-RunHdpxParallel-multiF-slow.R tests/testthat/test-RunHdpxParallel-multiT-slow.R tests/testthat/test-RunHdpxParallel-multitypeF-fast96-downsample.R tests/testthat/test-RunHdpxParallel-multitypeF-fast96.R tests/testthat/test-RunHdpxParallel-multitypeT-fast96.R tests/testthat/test-SaveAnalysis-fast.R tests/testthat/test-SetupAndPosterior.R tests/testthat/test-bad_output_dir.R
tests/testthat/test_AnalyzeAndPlotretval_out_dir/.gitignore
tests/testthat/test_AnalyzeAndPlotretval_out_dir/diagnostics.comp.size.pdf tests/testthat/test_AnalyzeAndPlotretval_out_dir/diagnostics.data.assigned.pdf tests/testthat/test_AnalyzeAndPlotretval_out_dir/diagnostics.likelihood.pdf tests/testthat/test_AnalyzeAndPlotretval_out_dir/diagnostics.numcluster.pdf tests/testthat/test_AnalyzeAndPlotretval_out_dir/diagnostics.signatures.pdf tests/testthat/test_AnalyzeAndPlotretval_out_dir/extracted.signature.pdf
tests/testthat/test_AnalyzeAndPlotretval_out_dir/extracted.signatures.csv
tests/testthat/test_AnalyzeAndPlotretval_out_dir/hdp.retval.Rdata
tests/testthat/test_AnalyzeAndPlotretval_out_dir/inferred.exposure.count.pdf tests/testthat/test_AnalyzeAndPlotretval_out_dir/inferred.exposure.proportion.pdf
tests/testthat/test_AnalyzeAndPlotretval_out_dir/inferred.exposures.csv
tests/testthat/test_RunHdpParallel-fast96_out_dir/diagnostics.comp.size.pdf tests/testthat/test_RunHdpParallel-fast96_out_dir/diagnostics.data.assigned.pdf tests/testthat/test_RunHdpParallel-fast96_out_dir/diagnostics.likelihood.pdf tests/testthat/test_RunHdpParallel-fast96_out_dir/diagnostics.numcluster.pdf tests/testthat/test_RunHdpParallel-fast96_out_dir/diagnostics.signatures.pdf
tests/testthat/test_RunHdpParallel-fast96_out_dir/hdp.retval.Rdata
tests/testthat/test_Runhdp4-fast96_out_dir/Runhdp4.retval.Rdata
tests/testthat/test_Runhdp4-fast96_out_dir/call.and.session.info.txt
tests/testthat/test_Runhdp4-fast96_out_dir/chlist.Rdata
tests/testthat/test_Runhdp4-fast96_out_dir/diagnostics.comp.size.pdf tests/testthat/test_Runhdp4-fast96_out_dir/diagnostics.data.assigned.pdf tests/testthat/test_Runhdp4-fast96_out_dir/diagnostics.likelihood.pdf tests/testthat/test_Runhdp4-fast96_out_dir/diagnostics.numcluster.pdf tests/testthat/test_Runhdp4-fast96_out_dir/diagnostics.signatures.pdf tests/testthat/test_Runhdp4-fast96_out_dir/extracted.signature.pdf
tests/testthat/test_Runhdp4-fast96_out_dir/extracted.signatures.csv
tests/testthat/test_Runhdp4-fast96_out_dir/inferred.exposure.count.pdf tests/testthat/test_Runhdp4-fast96_out_dir/inferred.exposure.proportion.pdf
tests/testthat/test_Runhdp4-fast96_out_dir/inferred.exposures.csv
tests/testthat/test_downsample_specta.R
vignettes/.gitignore
vignettes/mSigHdp.Rmd
steverozen/mSigHdp documentation built on Feb. 6, 2023, 1:36 a.m.

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