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FilterFFPE

This is the released version of FilterFFPE; for the devel version, see FilterFFPE.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12

FFPE Artificial Chimeric Read Filter for NGS data

DOI: 10.18129/B9.bioc.FilterFFPE

Bioconductor version: Release (3.23)

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] ORCID: 0000-0002-4281-8017

Maintainer: Lanying Wei <lanying.wei at uni-muenster.de>

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

Lanying Wei. FilterFFPE: FFPE Artificial Chimeric Read Filter for NGS data. doi:10.18129/B9.bioc.FilterFFPE, R package version 1.22.0, https://bioconductor.org/packages/FilterFFPE.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

Details

Package Archives

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