CNVfilteR
Identifies false positives of CNV calling tools by using SNV calls
Bioconductor version: Release (3.20)
CNVfilteR identifies those CNVs that can be discarded by using the single nucleotide variant (SNV) calls that are usually obtained in common NGS pipelines.
Author: Jose Marcos Moreno-Cabrera [aut, cre] , Bernat Gel [aut]
Maintainer: Jose Marcos Moreno-Cabrera <jpuntomarcos at gmail.com>
Citation (from within R, enter
citation("CNVfilteR")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CNVfilteR")
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("CNVfilteR")
CNVfilteR vignette | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | CopyNumberVariation, DNASeq, DataImport, Sequencing, Software, Visualization |
Version | 1.20.0 |
In Bioconductor since | BioC 3.10 (R-3.6) (5 years) |
License | Artistic-2.0 |
Depends | R (>= 4.3) |
Imports | IRanges, GenomicRanges, SummarizedExperiment, pracma, regioneR, assertthat, karyoploteR, CopyNumberPlots, graphics, utils, VariantAnnotation, Rsamtools, GenomeInfoDb, Biostrings, methods |
System Requirements | |
URL | https://github.com/jpuntomarcos/CNVfilteR |
Bug Reports | https://github.com/jpuntomarcos/CNVfilteR/issues |
See More
Suggests | knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, rmarkdown |
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 | CNVfilteR_1.20.0.tar.gz |
Windows Binary (x86_64) | CNVfilteR_1.20.0.zip |
macOS Binary (x86_64) | CNVfilteR_1.20.0.tgz |
macOS Binary (arm64) | CNVfilteR_1.19.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/CNVfilteR |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CNVfilteR |
Bioc Package Browser | https://code.bioconductor.org/browse/CNVfilteR/ |
Package Short Url | https://bioconductor.org/packages/CNVfilteR/ |
Package Downloads Report | Download Stats |