SARC

Statistical Analysis of Regions with CNVs

Bioconductor version: Release (3.20)

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>

Citation (from within R, enter citation("SARC")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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")

SARC	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CopyNumberVariation, DNASeq, Sequencing, Software, Visualization
Version	1.4.0
In Bioconductor since	BioC 3.18 (R-4.3) (1 year)
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
System Requirements
URL	https://github.com/Krutik6/SARC/
Bug Reports	https://github.com/Krutik6/SARC/issues

Suggests	knitr, kableExtra, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, Homo.sapiens, TxDb.Mmusculus.UCSC.mm10.knownGene, Mus.musculus, GenomicAlignments
Linking To
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Depends On Me
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Build Report	Build Report

Package Archives

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

Source Package	SARC_1.4.0.tar.gz
Windows Binary (x86_64)	SARC_1.4.0.zip (64-bit only)
macOS Binary (x86_64)	SARC_1.4.0.tgz
macOS Binary (arm64)	SARC_1.4.0.tgz
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