FilterFFPE

DOI: 10.18129/B9.bioc.FilterFFPE    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see FilterFFPE.

FFPE Artificial Chimeric Read Filter for NGS data

Bioconductor version: 3.12

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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	1.0.0
In Bioconductor since	BioC 3.12 (R-4.0) (0.5 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_1.0.0.tar.gz
Windows Binary	FilterFFPE_1.0.0.zip
macOS 10.13 (High Sierra)	FilterFFPE_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/FilterFFPE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/FilterFFPE
Package Short Url	https://bioconductor.org/packages/FilterFFPE/
Package Downloads Report	Download Stats