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FilterFFPE

FFPE Artificial Chimeric Read Filter for NGS data

Bioconductor version: Release (3.17)

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 "4.3") 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

Details

biocViews Alignment, Preprocessing, QualityControl, Sequencing, Software, StructuralVariation
Version 1.10.0
In Bioconductor since BioC 3.12 (R-4.0) (3 years)
License LGPL-3
Depends
Imports foreach, doParallel, GenomicRanges, IRanges, Rsamtools, parallel, S4Vectors
Linking To
Suggests BiocStyle
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Build Report  

Package Archives

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

Source Package FilterFFPE_1.10.0.tar.gz
Windows Binary FilterFFPE_1.10.0.zip (64-bit only)
macOS Binary (x86_64) FilterFFPE_1.10.0.tgz
macOS Binary (arm64) FilterFFPE_1.10.0.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