Files in broadinstitute/ichorCNA
A tool for estimating the fraction of tumor in ultra-low-pass whole genome sequencing (ULP-WGS) of cell-free DNA
.Rbuildignore
.Rinstignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
R/EM.R
R/output.R
R/plotting.R
R/segmentation.R
R/utils.R
README.md
inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt
inst/extdata/GRCh38.GCA_000001405.2_centromere_acen.txt
inst/extdata/HD_ULP_PoN_1Mb_median_normAutosome_mapScoreFiltered_median.rds
inst/extdata/HD_ULP_PoN_500kb_median_normAutosome_mapScoreFiltered_median.rds
inst/extdata/HD_ULP_PoN_hg38_1Mb_median_normAutosome_median.rds
inst/extdata/HD_ULP_PoN_hg38_500kb_median_normAutosome_median.rds
inst/extdata/MBC_315.ctDNA.reads.wig
inst/extdata/MBC_315_T2.ctDNA.reads.wig
inst/extdata/cytoBand_hg38.txt
inst/extdata/gc_hg19_1000kb.wig
inst/extdata/gc_hg19_10kb.wig
inst/extdata/gc_hg19_500kb.wig
inst/extdata/gc_hg19_50kb.wig
inst/extdata/gc_hg38_1000kb.wig
inst/extdata/gc_hg38_10kb.wig
inst/extdata/gc_hg38_500kb.wig
inst/extdata/gc_hg38_50kb.wig
inst/extdata/map_hg19_1000kb.wig
inst/extdata/map_hg19_10kb.wig
inst/extdata/map_hg19_500kb.wig
inst/extdata/map_hg19_50kb.wig
inst/extdata/map_hg38_1000kb.wig
inst/extdata/map_hg38_10kb.wig
inst/extdata/map_hg38_500kb.wig
inst/extdata/map_hg38_50kb.wig
man/ichorCNA-package.Rd
scripts/README.md
scripts/createPanelOfNormals.R
scripts/example_gw_plot.png
scripts/runIchorCNA.R
scripts/snakemake/README.md
scripts/snakemake/config/cluster.sh
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/config_hg38.yaml
scripts/snakemake/config/samples.yaml
scripts/snakemake/ichorCNA.snakefile
