Package: FilterFFPE 1.23.0

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_1.23.0.tar.gz
FilterFFPE_1.23.0.zip(r-4.7)FilterFFPE_1.23.0.zip(r-4.6)FilterFFPE_1.23.0.zip(r-4.5)
FilterFFPE_1.23.0.tgz(r-4.6-any)FilterFFPE_1.23.0.tgz(r-4.5-any)
FilterFFPE_1.23.0.tar.gz(r-4.7-any)FilterFFPE_1.23.0.tar.gz(r-4.6-any)
FilterFFPE_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
FilterFFPE/json (API)

# Install 'FilterFFPE' in R:

install.packages('FilterFFPE', repos = c('https://bioc.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.

structuralvariation sequencing alignment qualitycontrol preprocessing

3.30 score 1 scripts 1 mentions 3 exports 24 dependencies

Last updated from:b5ae7a79d9. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	167
linux-devel-x86_64	OK	252
source / vignettes	OK	271
linux-release-x86_64	OK	271
macos-release-arm64	OK	197
macos-oldrel-arm64	OK	156
windows-devel	OK	202
windows-release	OK	204
windows-oldrel	OK	197
wasm-release	OK	138

Exports:FFPEReadFilter filterBamByReadNames findArtifactChimericReads

Dependencies:BH BiocGenerics BiocParallel Biostrings bitops codetools cpp11 crayon doParallel foreach formatR futile.logger futile.options generics GenomicRanges IRanges iterators lambda.r Rhtslib Rsamtools S4Vectors Seqinfo snow XVector

An introduction to FilterFFPE

1 Introduction | 2 Input | 3 Artifact Chimeric Read Filtration | A Session info

Rendered fromFilterFFPE.Rnwusingutils::Sweave

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
FFPE Artificial Chimeric Read Filter for NGS data	FilterFFPE-package FilterFFPE
Find and filter artifact chimeric reads in BAM file of FFPE sample	FFPEReadFilter
Filter reads from BAM file by read names	filterBamByReadNames
Find artifact chimeric reads in BAM file of FFPE sample	findArtifactChimericReads