FilterFFPE

DOI: 10.18129/B9.bioc.FilterFFPE    

FFPE Artificial Chimeric Read Filter for NGS data

Bioconductor version: Release (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>

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

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) (< 6 months)
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 (32- & 64-bit)
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

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