SARC
Statistical Analysis of Regions with CNVs
Bioconductor version: Release (3.18)
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("SARC")):
Installation
To install this package, start R (version "4.3") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CopyNumberVariation, DNASeq, Sequencing, Software, Visualization |
| Version | 1.0.0 |
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SARC_1.0.0.tar.gz |
| Windows Binary | SARC_1.0.0.zip (64-bit only) |
| macOS Binary (x86_64) | SARC_1.0.0.tgz |
| macOS Binary (arm64) | SARC_1.0.0.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 |