Package: FilterFFPE 1.17.0

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_1.17.0.tar.gz
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FilterFFPE_1.17.0.tgz(r-4.4-any)FilterFFPE_1.17.0.tgz(r-4.3-any)
FilterFFPE_1.17.0.tar.gz(r-4.5-noble)FilterFFPE_1.17.0.tar.gz(r-4.4-noble)
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FilterFFPE.pdf |FilterFFPE.html✨
FilterFFPE/json (API)
NEWS

# Install 'FilterFFPE' in R:

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

On BioConductor:FilterFFPE-1.17.0(bioc 3.21)FilterFFPE-1.16.0(bioc 3.20)

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 179 downloads 1 mentions 3 exports 35 dependencies

Last updated 2 months agofrom:494b4cf7a8. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 19 2024
R-4.5-win	OK	Dec 19 2024
R-4.5-linux	OK	Dec 19 2024
R-4.4-win	OK	Dec 19 2024
R-4.4-mac	OK	Dec 19 2024
R-4.3-win	OK	Dec 19 2024
R-4.3-mac	OK	Dec 19 2024

Exports:FFPEReadFilter filterBamByReadNames findArtifactChimericReads

Dependencies:askpass BH BiocGenerics BiocParallel Biostrings bitops codetools cpp11 crayon curl doParallel foreach formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges httr IRanges iterators jsonlite lambda.r mime openssl R6 Rhtslib Rsamtools S4Vectors snow sys UCSC.utils XVector zlibbioc

An introduction to FilterFFPE

Rendered fromFilterFFPE.Rnwusingutils::Sweaveon Dec 19 2024.

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