Files in Wedge-Oxford/battenberg
Battenberg subclonal copy number caller
.github/workflows/r_checks.yml
DESCRIPTION
Dockerfile
LICENSE
NAMESPACE
R/Battenberg-package.R
R/battenberg.R
R/clonal_ascat.R
R/fastPCF.R
R/fitcopynumber.R
R/haplotype.R
R/haplotype_external.R
R/impute.R
R/orderEdges.R
R/plotting.R
R/prepare_SNP6.R
R/prepare_wgs.R
R/prepare_wgs_cell_line.R
R/segmentation.R
R/util.R
R/zzz.R
README.md
gcCorrect_chromosome_coordinates_hg19.txt
inst/TODO
inst/example/battenberg_allelecount.R
inst/example/battenberg_cleanup.sh
inst/example/battenberg_snp6.R
inst/example/battenberg_snp6_refitting.R
inst/example/battenberg_wgs.R
inst/example/filter_sv_brass.R
inst/example/parse_svs.R
inst/extdata/flat_subclones.txt
inst/extdata/template_rho_psi.txt
man/GetChromosomeBAFs.Rd
man/GetChromosomeBAFs_SNP6.Rd
man/allele_ratio_plot.Rd
man/battenberg.Rd
man/calc_rho_psi_refit.Rd
man/callChrXsubclones.Rd
man/callSubclones.Rd
man/call_multisample_MSAI.Rd
man/cel2baf.logr.Rd
man/check.imputeinfofile.Rd
man/cnfit_to_refit_suggestions.Rd
man/combine.baf.files.Rd
man/combine.impute.output.Rd
man/convert.impute.input.to.beagle.input.Rd
man/coverage_plot.Rd
man/fit.copy.number.Rd
man/gc.correct.Rd
man/gc.correct.wgs.Rd
man/generate.impute.input.snp6.Rd
man/generate.impute.input.wgs.Rd
man/get.chrom.names.Rd
man/getAlleleCounts.Rd
man/getBAFsAndLogRs.Rd
man/get_multisample_phasing.Rd
man/infer_gender_birdseed.Rd
man/input_known_haplotypes.Rd
man/make_posthoc_plots.Rd
man/mask_high_cn_segments.Rd
man/parse.imputeinfofile.Rd
man/plot.haplotype.data.Rd
man/prepare_snp6.Rd
man/prepare_wgs.Rd
man/read_alleleFrequencies.Rd
man/read_baf.Rd
man/read_bafsegmented.Rd
man/read_beagle_output.Rd
man/read_gccontent.Rd
man/read_impute_input.Rd
man/read_imputed_output.Rd
man/read_logr.Rd
man/read_replication.Rd
man/read_table_generic.Rd
man/run.beagle5.Rd
man/run.impute.Rd
man/run_haplotyping.Rd
man/segment.baf.phased.Rd
man/segment.baf.phased.legacy.Rd
man/segment.baf.phased.multisample.Rd
man/segment.baf.phased.sv.Rd
man/split_input_haplotypes.Rd
man/squaresplot.Rd
man/suggest_refit.Rd
man/totalcn_chrom_plot.Rd
man/write_battenberg_phasing.Rd
man/writebeagle.as.impute.Rd
man/writevcf.beagle.Rd
