CNVfilteR
Identifies false positives of CNV calling tools by using SNV calls
Bioconductor version: 3.24 · Package version: 1.27.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
CNVfilteR identifies those CNVs that can be discarded by using the single nucleotide variant (SNV) calls that are usually obtained in common NGS pipelines.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CNVfilteR")Details
| Maintainer | Jose Marcos Moreno-Cabrera <jpuntomarcos@gmail.com> |
| Author | Jose Marcos Moreno-Cabrera [aut, cre] (ORCID: <https://orcid.org/0000-0001-8570-0345>), Bernat Gel [aut] |
| License | Artistic-2.0 |
| URL | https://github.com/jpuntomarcos/CNVfilteR |
| Bug Reports | https://github.com/jpuntomarcos/CNVfilteR/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | CopyNumberVariation, DNASeq, DataImport, Sequencing, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/CNVfilteR/ |
Citation
From within R, enter citation("CNVfilteR"):
Jose Marcos Moreno-Cabrera, Bernat Gel. CNVfilteR: Identifies false positives of CNV calling tools by using SNV calls. doi:10.18129/B9.bioc.CNVfilteR, R package version 1.27.0, https://bioconductor.org/packages/CNVfilteR.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | CNVfilteR_1.27.0.tar.gz |
| Windows binary (x86_64) | CNVfilteR_1.27.0.zip |
| macOS binary (arm64) | CNVfilteR_1.27.0.tgz |
| macOS binary (x86_64) | CNVfilteR_1.27.0.tgz |
Dependencies
Depends: R (>= 4.3)
Imports: IRanges, GenomicRanges, SummarizedExperiment, pracma, regioneR, assertthat, karyoploteR, CopyNumberPlots, graphics, utils, VariantAnnotation, Rsamtools, GenomeInfoDb, Biostrings, methods
Suggests: knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, rmarkdown