Files in Pitithat-pu/cfDNAkit
Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)
.gitignore
DESCRIPTION
NAMESPACE
R/calculate_CES_score.R
R/call_cnv.R
R/create_PoN.R
R/get_fragment_profile.R
R/get_solution_table.R
R/get_zscore_profile.R
R/plot_cnv_solution.R
R/plot_distance_matrix.R
R/plot_fragment_dist.R
R/plot_sl_ratio.R
R/plot_transformed_sl.R
R/read_bamfile.R
R/segmentByPSCB.R
R/utils-pipe.R
R/utils.R
README.md
inst/NEWS
inst/extdata/AnnotationDataFrame_from_QDNAseq_hg19_1000k.rds
inst/extdata/AnnotationDataFrame_from_QDNAseq_hg38_1000k.rds
inst/extdata/BH01_CHR15.SampleBam.rds
inst/extdata/ex.PoN.rds
inst/extdata/ex.healthy1.rds
inst/extdata/ex.healthy2.rds
inst/extdata/ex.plasma.bam
inst/extdata/example_patientcfDNA_SampleBam.RDS
inst/extdata/example_patientcfDNA_SampleFragment.RDS
inst/extdata/hg19_centromere.tsv.gz
inst/extdata/hg19_chrTotalLength.tsv
inst/extdata/hg38_chrTotalLength.tsv
inst/extdata/wgEncodeDacMapabilityConsensusExcludable.bed_GRCh37.gz
inst/script/DescriptionOfExtdata.md
inst/script/extractFragmentProfile.R
inst/script/run_cfdnakit.R
man/GRCh2UCSCGRanges.Rd
man/UCSC2GRChSampleBam.Rd
man/calculate_CES_score.Rd
man/call_cnv.Rd
man/cfdnakit-package.Rd
man/create_PoN.Rd
man/create_blacklist_gr.Rd
man/extract_insert_size.Rd
man/filter_read_on_blacklist.Rd
man/fragment_dist.Rd
man/get_fragment_profile.Rd
man/get_segment_bysolution.Rd
man/get_solution_table.Rd
man/get_zscore_profile.Rd
man/if_exist_baifile.Rd
man/if_ucsc_chrformat.Rd
man/make_density_table.Rd
man/overlap_bin_with_segment.Rd
man/pipe.Rd
man/plot_cnv_solution.Rd
man/plot_distance_matrix.Rd
man/plot_fragment_dist.Rd
man/plot_sl_ratio.Rd
man/plot_transformed_sl.Rd
man/read_PoN_files.Rd
man/read_bamfile.Rd
man/segmentByPSCB.Rd
man/test_isize_KolmogorovSmirnov.Rd
man/util.bias_correct.Rd
man/zscore_transform.Rd
vignettes/.gitignore
vignettes/cfdnakit-vignette.Rmd
