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 (from within R, enter 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	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

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

Suggests	BiocStyle
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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 (x86_64)	FilterFFPE_1.14.0.zip
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 [email protected]:packages/FilterFFPE
Bioc Package Browser	https://code.bioconductor.org/browse/FilterFFPE/
Package Short Url	https://bioconductor.org/packages/FilterFFPE/
Package Downloads Report	Download Stats