Package: SimFFPE 1.19.0
Lanying Wei
SimFFPE: NGS Read Simulator for FFPE Tissue
The NGS (Next-Generation Sequencing) reads from FFPE (Formalin-Fixed Paraffin-Embedded) samples contain numerous artifact chimeric reads (ACRS), which can lead to false positive structural variant calls. These ACRs are derived from the combination of two single-stranded DNA (ss-DNA) fragments with short reverse complementary regions (SRCRs). This package simulates these artifact chimeric reads as well as normal reads for FFPE samples on the whole genome / several chromosomes / large regions.
Authors:
SimFFPE_1.19.0.tar.gz
SimFFPE_1.19.0.zip(r-4.5)SimFFPE_1.19.0.zip(r-4.4)SimFFPE_1.19.0.zip(r-4.3)
SimFFPE_1.19.0.tgz(r-4.4-any)SimFFPE_1.19.0.tgz(r-4.3-any)
SimFFPE_1.19.0.tar.gz(r-4.5-noble)SimFFPE_1.19.0.tar.gz(r-4.4-noble)
SimFFPE_1.19.0.tgz(r-4.4-emscripten)SimFFPE_1.19.0.tgz(r-4.3-emscripten)
SimFFPE.pdf |SimFFPE.html✨
SimFFPE/json (API)
NEWS
| # Install 'SimFFPE' in R: |
| install.packages('SimFFPE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:SimFFPE-1.19.0(bioc 3.21)SimFFPE-1.18.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
sequencingalignmentmultiplecomparisonsequencematchingdataimport
Last updated 23 days agofrom:77724cf106. Checks:OK: 4 WARNING: 3. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | WARNING | Oct 31 2024 |
| R-4.5-linux | OK | Oct 31 2024 |
| R-4.4-win | WARNING | Oct 31 2024 |
| R-4.4-mac | OK | Oct 31 2024 |
| R-4.3-win | WARNING | Oct 31 2024 |
| R-4.3-mac | OK | Oct 31 2024 |
Exports:calcPhredScoreProfilereadSimFFPEtargetReadSimFFPE
Dependencies:askpassBHBiocGenericsBiocParallelBiostringsbitopsclicodetoolscpp11crayoncurldoParalleldplyrfansiforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesiteratorsjsonlitelambda.rlifecyclemagrittrmimeopensslpillarpkgconfigR6RhtslibrlangRsamtoolsS4VectorssnowsystibbletidyselecttruncnormUCSC.utilsutf8vctrswithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| NGS Read Simulator for FFPE Tissue | SimFFPE-package SimFFPE |
| Estimate Phred score profile for FFPE read simulation | calcPhredScoreProfile |
| Simulate normal and artifact chimeric reads in NGS data of FFPE samples for whole genome / several chromosomes / large regions | readSimFFPE |
| Simulate normal and artifact chimeric reads in NGS data of FFPE samples for exonic / targeted regions | targetReadSimFFPE |
