Package: cfdnakit 1.11.0

Pitithat Puranachot

cfdnakit: Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)

This package provides basic functions for analyzing shallow whole-genome sequencing (~0.3X or more) of cell-free DNA (cfDNA). The package basically extracts the length of cfDNA fragments and aids the vistualization of fragment-length information. The package also extract fragment-length information per non-overlapping fixed-sized bins and used it for calculating ctDNA estimation score (CES).

Authors:Pitithat Puranachot [aut, cre]

cfdnakit_1.11.0.tar.gz
cfdnakit_1.11.0.zip(r-4.7)cfdnakit_1.11.0.zip(r-4.6)cfdnakit_1.11.0.zip(r-4.5)
cfdnakit_1.11.0.tgz(r-4.6-any)cfdnakit_1.11.0.tgz(r-4.5-any)
cfdnakit_1.11.0.tar.gz(r-4.7-any)cfdnakit_1.11.0.tar.gz(r-4.6-any)
cfdnakit_1.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cfdnakit/json (API)

# Install 'cfdnakit' in R:

install.packages('cfdnakit', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pitithat-pu/cfdnakit/issues

On BioConductor:cfdnakit-1.11.0(bioc 3.24)cfdnakit-1.10.0(bioc 3.23)

copynumbervariation sequencing wholegenome

5.00 score 9 stars 11 scripts 319 downloads 15 exports 76 dependencies

Last updated from:bfe08ee281. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	183
linux-devel-x86_64	OK	349
source / vignettes	OK	265
linux-release-x86_64	OK	283
macos-release-arm64	OK	208
macos-oldrel-arm64	OK	228
windows-devel	OK	285
windows-release	OK	286
windows-oldrel	OK	254
wasm-release	OK	153

Exports:calculate_CES_score call_cnv create_PoN extract_insert_size get_fragment_profile get_solution_table get_zscore_profile plot_cnv_solution plot_distance_matrix plot_fragment_dist plot_sl_ratio plot_transformed_sl read_bamfile segmentByPSCB test_isize_KolmogorovSmirnov

Dependencies:aroma.light askpass BH Biobase BiocGenerics BiocParallel Biostrings bitops CGHbase CGHcall cli codetools cpp11 crayon curl digest DNAcopy dplyr farver formatR futile.logger futile.options future future.apply generics GenomeInfoDb GenomicRanges ggplot2 globals glue gtable httr impute IRanges isoband jsonlite labeling lambda.r lifecycle limma listenv magrittr marray matrixStats mime openssl parallelly pillar pkgconfig PSCBS QDNAseq R.cache R.methodsS3 R.oo R.utils R6 RColorBrewer Rhtslib rlang Rsamtools S4Vectors S7 scales Seqinfo snow snowfall statmod sys tibble tidyselect UCSC.utils utf8 vctrs viridisLite withr XVector

cfdnakit vignette

Rendered fromcfdnakit-vignette.Rmdusingknitr::rmarkdown

Last update: 2023-05-27
Started: 2022-11-09

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)	cfdnakit-package cfdnakit
Calculate CES Score from Segmentation	calculate_CES_score
Call Copy-number Variation from SLRatio and segmentation	call_cnv
Create Blacklist regions GRanges object	create_blacklist_gr
Create Panel-of-Normal (PoN) object	create_PoN
Extract Insert size from SampleBam	extract_insert_size
Filter out reads on blacklist regions	filter_read_on_blacklist
Get insert-size distribution table	fragment_dist
Getting fragment-length information	get_fragment_profile
Return CNV segmentation result from given all CNV solutions	get_segment_bysolution
Get summarised table of cnv solutions	get_solution_table
Transform SLRatio with PoN Fragment profile	get_zscore_profile
Convert GRCh chromosome format to UCSC style	GRCh2UCSCGRanges
Check if bai file exist from given bam	if_exist_baifile
Check UCSC chromosomes format for input bam file	if_ucsc_chrformat
Make Fragment-length density table	make_density_table
Overlap and merge bin data frame with segmentation dataframe	overlap_bin_with_segment
Plot Fragment-length profile with CNV calling result	plot_cnv_solution
Plot Distance Matrix from CNVCalling	plot_distance_matrix
Plot Fragment-length Distribution	plot_fragment_dist
Plot Short/Long-fragment Ratio	plot_sl_ratio
Plot z-tranformed Short/Long-fragment Ratio	plot_transformed_sl
Read a bam file Read a bam file from give path. Alignment and sequencing read information will be binned into non-overlapping size	read_bamfile
Read Fragment Profile from a list of rds file	read_PoN_files
Segmentation data with PSCBS	segmentByPSCB
KolmogorovSmirnov test for insert size	test_isize_KolmogorovSmirnov
Convert UCSC chromosome format to GRCh style from a list of alignment information	UCSC2GRChSampleBam
Correct GC Bias readcount	util.bias_correct
zscore_transform transforms SLRatio profile into z-score	zscore_transform