1 Introduction | 2 Input | 3 Simulation | A Session info
Package: SimFFPE 1.25.0
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_1.25.0.tar.gz
SimFFPE_1.25.0.zip(r-4.7)SimFFPE_1.25.0.zip(r-4.6)SimFFPE_1.25.0.zip(r-4.5)
SimFFPE_1.25.0.tgz(r-4.6-any)SimFFPE_1.25.0.tgz(r-4.5-any)
SimFFPE_1.25.0.tar.gz(r-4.7-any)SimFFPE_1.25.0.tar.gz(r-4.6-any)
SimFFPE_1.25.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SimFFPE/json (API)
| # Install 'SimFFPE' in R: |
| install.packages('SimFFPE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:SimFFPE-1.25.0(bioc 3.24)SimFFPE-1.24.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
sequencingalignmentmultiplecomparisonsequencematchingdataimport
Last updated from:f626f0c8b8. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 175 | ||
| linux-devel-x86_64 | OK | 281 | ||
| source / vignettes | OK | 269 | ||
| linux-release-x86_64 | OK | 339 | ||
| macos-release-arm64 | OK | 155 | ||
| macos-oldrel-arm64 | OK | 148 | ||
| windows-devel | OK | 238 | ||
| windows-release | OK | 259 | ||
| windows-oldrel | OK | 247 | ||
| wasm-release | OK | 113 |
Exports:calcPhredScoreProfilereadSimFFPEtargetReadSimFFPE
Dependencies:BHBiocGenericsBiocParallelBiostringsbitopsclicodetoolscpp11crayondoParalleldplyrforeachformatRfutile.loggerfutile.optionsgenericsGenomicRangesglueIRangesiteratorslambda.rlifecyclemagrittrpillarpkgconfigR6RhtslibrlangRsamtoolsS4VectorsSeqinfosnowtibbletidyselecttruncnormutf8vctrswithrXVector
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 |
