Files in gavinha/TitanCNA
Subclonal copy number and LOH prediction from whole genome sequencing of tumours
.Rbuildignore
.Rinstignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/correction.R
R/haplotype.R
R/hmmClonal.R
R/paramEstimation.R
R/plotting.R
R/utils.R
R/zzz.R
README.md
data/EMresults.rda
data/datalist
inst/CITATION
inst/extdata/Seqinfo_hg19.rda
inst/extdata/gc_chr2.wig
inst/extdata/map_chr2.wig
inst/extdata/test_alleleCounts_chr2.txt
inst/extdata/test_norm_chr2.wig
inst/extdata/test_tum_chr2.wig
man/TitanCNA-dataset.Rd
man/TitanCNA-output.Rd
man/TitanCNA-package.Rd
man/TitanCNA-plotting.Rd
man/computeSDbwIndex.Rd
man/correctCN.Rd
man/correctReadDepth.Rd
man/filterData.Rd
man/getPositionOverlap.Rd
man/haplotype.Rd
man/loadAlleleCounts.Rd
man/loadDefaultParameters.Rd
man/runEMclonalCN.Rd
man/viterbiClonalCN.Rd
man/wigImport.Rd
scripts/README.md
scripts/R_scripts/README.md
scripts/R_scripts/selectSolution.R
scripts/R_scripts/titanCNA.R
scripts/TenX_scripts/README.md
scripts/TenX_scripts/data/10kb.bed.tar.gz
scripts/TenX_scripts/data/GRCh37.p13_centromere_UCSC-gapTable.txt
scripts/TenX_scripts/data/gc_hg19_10kb.wig
scripts/TenX_scripts/data/map_hg19_10kb.wig
scripts/TenX_scripts/getMoleculeCoverage.R
scripts/TenX_scripts/getPhasedHETSitesFromLLRVCF.R
scripts/TenX_scripts/getTumourAlleleCountsAtHETSites.py
scripts/TenX_scripts/titanCNA_v1.15.0_TenX.R
scripts/snakemake/README.md
scripts/snakemake/TitanCNA.snakefile
scripts/snakemake/code/combineTITAN-ichor.R
scripts/snakemake/code/countPysam.py
scripts/snakemake/config/cluster_qsub.sh
scripts/snakemake/config/cluster_qsub.yaml
scripts/snakemake/config/cluster_slurm.yaml
scripts/snakemake/config/config.yaml
scripts/snakemake/config/samples.yaml
scripts/snakemake/getAlleleCounts.snakefile
scripts/snakemake/ichorCNA.snakefile
src/fwd_backC_clonalCN.c
src/getPositionOverlapC.c
src/register.c
src/titan.h
src/viterbiC_clonalCN.c
vignettes/TitanCNA.Rnw
vignettes/TitanCNA.bib
