CNVfilteR
This is thereleased version of CNVfilteR; for the devel version, seeCNVfilteR.
Identifies false positives of CNV calling tools by using SNV calls
Bioconductor version: Release (3.22)
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]
ORCID: 0000-0001-8570-0345, 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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("CNVfilteR")For older versions of R, please refer to the appropriateBioconductor 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 | 1.24.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (6 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
FollowInstallation instructions to use this package in your R session.
| Source Package | CNVfilteR_1.24.0.tar.gz |
| Windows Binary (x86_64) | CNVfilteR_1.24.0.zip |
| macOS Binary (x86_64) | CNVfilteR_1.24.0.tgz |
| macOS Binary (arm64) | CNVfilteR_1.24.0.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 |