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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>

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


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Reference Manual PDF


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
System Requirements
URL https://github.com/Krutik6/SARC/
Bug Reports https://github.com/Krutik6/SARC/issues
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Suggests knitr, kableExtra, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, Homo.sapiens, TxDb.Mmusculus.UCSC.mm10.knownGene, Mus.musculus, GenomicAlignments
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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) SARC_1.1.0.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/
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