SARC

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

Statistical Analysis of Regions with CNVs


Bioconductor version: Development (3.20)

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")

# 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")
SARC HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews CopyNumberVariation, DNASeq, Sequencing, Software, Visualization
Version 1.3.0
In Bioconductor since BioC 3.18 (R-4.3) (0.5 years)
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
See More
Suggests knitr, kableExtra, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, Homo.sapiens, TxDb.Mmusculus.UCSC.mm10.knownGene, Mus.musculus, GenomicAlignments
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Package Archives

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

Source Package SARC_1.3.0.tar.gz
Windows Binary SARC_1.3.0.zip
macOS Binary (x86_64) SARC_1.3.0.tgz
macOS Binary (arm64) SARC_1.3.0.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