FilterFFPE
FFPE Artificial Chimeric Read Filter for NGS data
Bioconductor version: Release (3.19)
This package finds and filters artificial chimeric reads specifically generated in next-generation sequencing (NGS) process of formalin-fixed paraffin-embedded (FFPE) tissues. These artificial chimeric reads can lead to a large number of false positive structural variation (SV) calls. The required input is an indexed BAM file of a FFPE sample.
Author: Lanying Wei [aut, cre]
Maintainer: Lanying Wei <lanying.wei at uni-muenster.de>
citation("FilterFFPE")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("FilterFFPE")
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("FilterFFPE")
An introduction to FilterFFPE | R Script | |
Reference Manual | ||
NEWS | Text |
Details
biocViews | Alignment, Preprocessing, QualityControl, Sequencing, Software, StructuralVariation |
Version | 1.14.0 |
In Bioconductor since | BioC 3.12 (R-4.0) (4 years) |
License | LGPL-3 |
Depends | |
Imports | foreach, doParallel, GenomicRanges, IRanges, Rsamtools, parallel, S4Vectors |
System Requirements | |
URL |
See More
Suggests | BiocStyle |
Linking To | |
Enhances | |
Depends On Me | |
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Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | FilterFFPE_1.14.0.tar.gz |
Windows Binary | FilterFFPE_1.14.0.zip (64-bit only) |
macOS Binary (x86_64) | FilterFFPE_1.14.0.tgz |
macOS Binary (arm64) | FilterFFPE_1.14.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/FilterFFPE |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/FilterFFPE |
Bioc Package Browser | https://code.bioconductor.org/browse/FilterFFPE/ |
Package Short Url | https://bioconductor.org/packages/FilterFFPE/ |
Package Downloads Report | Download Stats |