SARC

DOI: 10.18129/B9.bioc.SARC  

This is the development version of SARC; for the stable release version, see SARC.

Statistical Analysis of Regions with CNVs

Bioconductor version: Development (3.19)

Imports a cov/coverage file (normalised read coverages from BAM files) and a cnv file (list of CNVs - similiar to a BED file) from WES/ WGS CNV (copy number variation) detection pipelines and utilises several metrics to weigh the likelihood of a sample containing a detected CNV being a true CNV or a false positive. Highly useful for diagnostic testing to filter out false positives to provide clinicians with fewer variants to interpret. SARC uniquely only used cov and csv (similiar to BED file) files which are the common CNV pipeline calling filetypes, and can be used as to supplement the Interactive Genome Browser (IGV) to generate many figures automatedly, which can be especially helpful in large cohorts with 100s-1000s of patients.

Author: Krutik Patel [aut, cre]

Maintainer: Krutik Patel <nkp68 at newcastle.ac.uk>

Installation

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("SARC")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SARC")

 

HTML	R Script	SARC
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	CopyNumberVariation, DNASeq, Sequencing, Software, Visualization
Version	1.1.0
In Bioconductor since	BioC 3.18 (R-4.3) (< 6 months)
License	GPL-3
Depends	R (>= 4.3), RaggedExperiment, GenomicRanges
Imports	tidyverse, utils, reshape2, DescTools, metap, multtest, plyranges, data.table, scales, RColorBrewer, grid, gtable, gridExtra, GenomicFeatures, stats, ggplot2, plotly, IRanges
LinkingTo
Suggests	knitr, kableExtra, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, Homo.sapiens, TxDb.Mmusculus.UCSC.mm10.knownGene, Mus.musculus, GenomicAlignments
SystemRequirements
Enhances
URL	https://github.com/Krutik6/SARC/
BugReports	https://github.com/Krutik6/SARC/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	SARC_1.1.0.tar.gz
Windows Binary	SARC_1.1.0.zip
macOS Binary (x86_64)	SARC_1.1.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/SARC
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SARC
Bioc Package Browser	https://code.bioconductor.org/browse/SARC/
Package Short Url	https://bioconductor.org/packages/SARC/
Package Downloads Report	Download Stats