FilterFFPE

DOI: 10.18129/B9.bioc.FilterFFPE  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see FilterFFPE.

FFPE Artificial Chimeric Read Filter for NGS data

Bioconductor version: 3.16

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 (from within R, enter citation("FilterFFPE")):

Installation

To install this package, start R (version "4.2") 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")

 

PDF R Script An introduction to FilterFFPE
PDF   Reference Manual
Text   NEWS

Details

biocViews Alignment, Preprocessing, QualityControl, Sequencing, Software, StructuralVariation
Version 1.8.0
In Bioconductor since BioC 3.12 (R-4.0) (2.5 years)
License LGPL-3
Depends
Imports foreach, doParallel, GenomicRanges, IRanges, Rsamtools, parallel, S4Vectors
LinkingTo
Suggests BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package FilterFFPE_1.8.0.tar.gz
Windows Binary FilterFFPE_1.8.0.zip (64-bit only)
macOS Binary (x86_64) FilterFFPE_1.8.0.tgz
macOS Binary (arm64) FilterFFPE_1.8.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: