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This is the development version of cfdnakit; for the stable release version, see cfdnakit.
Bioconductor version: Development (3.19)
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).
Author: Pitithat Puranachot [aut, cre]
Maintainer: Pitithat Puranachot <pitithat at gmail.com>
Citation (from within R,
enter citation("cfdnakit")
):
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # The following initializes usage of Bioc devel BiocManager::install(version='devel') BiocManager::install("cfdnakit")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cfdnakit")
HTML | R Script | cfdnakit vignette |
Reference Manual | ||
Text | NEWS |
biocViews | CopyNumberVariation, Sequencing, Software, WholeGenome |
Version | 1.1.0 |
In Bioconductor since | BioC 3.18 (R-4.3) (< 6 months) |
License | GPL-3 |
Depends | R (>= 4.3) |
Imports | Biobase, dplyr, GenomicRanges, GenomeInfoDb, ggplot2, IRanges, magrittr, PSCBS, QDNAseq, Rsamtools, utils, S4Vectors, stats, rlang |
LinkingTo | |
Suggests | rmarkdown, knitr, roxygen2, BiocStyle |
SystemRequirements | |
Enhances | |
URL | |
BugReports | https://github.com/Pitithat-pu/cfdnakit/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | cfdnakit_1.1.0.tar.gz |
Windows Binary | cfdnakit_1.1.0.zip |
macOS Binary (x86_64) | cfdnakit_1.1.0.tgz |
macOS Binary (arm64) | |
Source Repository | git clone https://git.bioconductor.org/packages/cfdnakit |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/cfdnakit |
Bioc Package Browser | https://code.bioconductor.org/browse/cfdnakit/ |
Package Short Url | https://bioconductor.org/packages/cfdnakit/ |
Package Downloads Report | Download Stats |
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