CNVfilteR
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see CNVfilteR.
Identifies false positives of CNV calling tools by using SNV calls
Bioconductor version: 3.10
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 <jmoreno at igtp.cat> and Bernat Gel <bgel at igtp.cat>
Maintainer: Jose Marcos Moreno-Cabrera <jmoreno at igtp.cat>
citation("CNVfilteR")):
Installation
To install this package, start R (version "3.6") 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 | 1.0.4 |
| In Bioconductor since | BioC 3.10 (R-3.6) (4.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.6) |
| Imports | IRanges, GenomicRanges, SummarizedExperiment, pracma, regioneR, assertthat, karyoploteR, CopyNumberPlots, graphics, utils, VariantAnnotation, Rsamtools, GenomeInfoDb, Biostrings, methods |
| System Requirements | |
| URL | https://github.com/jpuntomarcos/CNVfilteR |
See More
| Suggests | knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked |
| 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_1.0.4.tar.gz |
| Windows Binary | CNVfilteR_1.0.4.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | CNVfilteR_1.0.4.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 |
| Old Source Packages for BioC 3.10 | Source Archive |