Package: FilterFFPE 1.22.0

Lanying Wei

FilterFFPE: FFPE Artificial Chimeric Read Filter for NGS data

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.

Authors:Lanying Wei [aut, cre]

FilterFFPE_1.22.0.tar.gz
FilterFFPE_1.22.0.zip(r-4.7)FilterFFPE_1.22.0.zip(r-4.6)FilterFFPE_1.22.0.zip(r-4.5)
FilterFFPE_1.22.0.tgz(r-4.6-any)FilterFFPE_1.22.0.tgz(r-4.5-any)
FilterFFPE_1.22.0.tar.gz(r-4.7-any)FilterFFPE_1.22.0.tar.gz(r-4.6-any)
FilterFFPE_1.22.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
FilterFFPE/json (API)
NEWS

# Install 'FilterFFPE' in R:
install.packages('FilterFFPE', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:FilterFFPE-1.23.0(bioc 3.24)FilterFFPE-1.22.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

structuralvariationsequencingalignmentqualitycontrolpreprocessing

3.30 score 3 scripts 316 downloads 1 mentions 3 exports 24 dependencies

Last updated from:22159a2ce7 (on RELEASE_3_23). Checks:1 WARNING, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING147
linux-devel-x86_64OK256
source / vignettesOK271
linux-release-x86_64OK246
macos-release-arm64OK239
macos-oldrel-arm64OK176
windows-develOK207
windows-releaseOK204
windows-oldrelOK256
wasm-releaseOK127

Exports:FFPEReadFilterfilterBamByReadNamesfindArtifactChimericReads

Dependencies:BHBiocGenericsBiocParallelBiostringsbitopscodetoolscpp11crayondoParallelforeachformatRfutile.loggerfutile.optionsgenericsGenomicRangesIRangesiteratorslambda.rRhtslibRsamtoolsS4VectorsSeqinfosnowXVector

An introduction to FilterFFPE

Rendered fromFilterFFPE.Rnwusingutils::Sweaveon Jun 02 2026.

Last update: 2020-11-11
Started: 2020-09-18