Files in junseonghwan/ScRNACloneEvaluation
ScRNA clone evaluation.
.Rbuildignore
.gitignore
.gitmodules
DESCRIPTION
Laks/Config.txt
Laks/ConfigLocal.txt
Laks/GeneratePseudoBulk.py
Laks/MergeBAMs.sh
Laks/README.md
Laks/Rscripts/ExtractExonicSNV.R
Laks/Rscripts/GenerateBulkInput.R
Laks/Strelka.py
Laks/Strelka.sh
NAMESPACE
R/.Rhistory
R/CellAssign.R
R/EDA.R
R/EvaluationFunctions.R
R/FindClones.R
R/RcppExports.R
R/VAFclusterEM.R
R/bestAICsearch.R
README.md
Tirosh/Config.txt
Tirosh/ConfigLocal.txt
Tirosh/GenerateBulkInput.R
Tirosh/GenerateScInput.R
Tirosh/IdentifySNV.R
Tirosh/TitanCNA.snakefile
Tirosh/cluster_slurm.yaml
Tirosh/config.yaml
Tirosh/getAlleleCounts.snakefile
Tirosh/ichorCNA.snakefile
Tirosh/samples.yaml
man/.Rapp.history
man/VAFclusterEM.Rd
man/bestAICsearch.Rd
scripts/ExtractReadCounts.py
scripts/ExtractReadCounts.sh
scripts/GenerateInputForSimulatedStudy.py
scripts/GenerateInputForSimulatedStudy.sh
scripts/Rscripts/ExtractReadCounts.R
scripts/Rscripts/GenerateBulkInput.R
scripts/Rscripts/GenerateInputForBScite.R
scripts/Rscripts/GenerateInputForSimulatedStudy.R
scripts/Rscripts/GenerateScInput.R
scripts/Rscripts/RunDDClone.R
scripts/RunAlleleCounts.sh
scripts/RunBScite.py
scripts/RunDDClone.py
scripts/RunDDClone.sh
scripts/RunGenerateDataScript.sh
scripts/RunIchor.sh
scripts/RunLaks.py
scripts/RunLaks.sh
scripts/RunPhyloWGS.py
scripts/RunPhyloWGS.sh
scripts/RunSimulationStudy.py
scripts/RunSimulationStudy.sh
scripts/RunTitan.sh
scripts/ScVariantCaller.py
scripts/ScVariantCaller.sh
scripts/StrelkaGenome.sh
simulated/Binary/ExtractPhyloWGSResults.py
simulated/Binary/ExtractPhyloWGSResultsLocally.sh
simulated/Binary/Figures/Main.R
simulated/Binary/Rscripts/ComputeAncestralMetric.R
simulated/Binary/Rscripts/ExtractPhyloWGSResults.R
simulated/Binary/Rscripts/GenerateInputForBScite.R
simulated/Binary/Rscripts/GenerateInputForPhyloWGS.R
simulated/Binary/Rscripts/GenerateInputForSimulatedStudy.R
simulated/Binary/Rscripts/ProcessBSCITEResults.R
simulated/Binary/Rscripts/RunCanopy.R
simulated/Binary/Rscripts/RunDDClone.R
simulated/Binary/RunBSCITE.py
simulated/Binary/RunBSCITE.sh
simulated/Binary/RunCanopy.py
simulated/Binary/RunCanopy.sh
simulated/Binary/RunDDClone.py
simulated/Binary/RunDDClone.sh
simulated/Binary/RunPhyloWGS.py
simulated/Binary/RunPhyloWGS.sh
simulated/Binary/RunPhyloWGSLocally.sh
simulated/Binary/RunSimulationStudy.py
simulated/Binary/RunSimulationStudy.sh
simulated/Binary/RunSimulationStudyLocally.sh
simulated/Binary/simul.config
simulated/Cherry/ExtractPhyloWGSResults.py
simulated/Cherry/ExtractPhyloWGSResultsLocally.sh
simulated/Cherry/Figures/Main.R
simulated/Cherry/Rscripts/ExtractPhyloWGSResults.R
simulated/Cherry/Rscripts/GenerateInputForPhyloWGS.R
simulated/Cherry/Rscripts/GenerateInputForSimulatedStudy.R
simulated/Cherry/RunPhyloWGS.py
simulated/Cherry/RunPhyloWGSLocally.sh
simulated/Cherry/RunSimulationStudy.py
simulated/Cherry/RunSimulationStudyLocally.sh
simulated/Cherry/simul.config
src/.gitignore
src/RcppExports.cpp
src/node.cpp
src/node.hpp
src/numerical_utils.cpp
src/numerical_utils.hpp
src/rcpp_hello_world.cpp
