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:
FilterFFPE_1.17.0.tar.gz
FilterFFPE_1.17.0.zip(r-4.5)FilterFFPE_1.17.0.zip(r-4.4)FilterFFPE_1.17.0.zip(r-4.3)
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)
FilterFFPE_1.17.0.tgz(r-4.4-emscripten)FilterFFPE_1.17.0.tgz(r-4.3-emscripten)
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.
structuralvariationsequencingalignmentqualitycontrolpreprocessing
Last updated 22 days agofrom:494b4cf7a8. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 19 2024 |
| R-4.5-win | OK | Nov 19 2024 |
| R-4.5-linux | OK | Nov 19 2024 |
| R-4.4-win | OK | Nov 19 2024 |
| R-4.4-mac | OK | Nov 19 2024 |
| R-4.3-win | OK | Nov 19 2024 |
| R-4.3-mac | OK | Nov 19 2024 |
Exports:FFPEReadFilterfilterBamByReadNamesfindArtifactChimericReads
Dependencies:askpassBHBiocGenericsBiocParallelBiostringsbitopscodetoolscpp11crayoncurldoParallelforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesiteratorsjsonlitelambda.rmimeopensslR6RhtslibRsamtoolsS4VectorssnowsysUCSC.utilsXVectorzlibbioc
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 |
