Package: STRMPS 0.6.9
STRMPS: Analysis of Short Tandem Repeat (STR) Massively Parallel Sequencing (MPS) Data
Loading, identifying, aggregating, manipulating, and analysing short tandem repeat regions of massively parallel sequencing data in forensic genetics. The analyses and framework implemented in this package relies on the papers of Vilsen et al. (2017) <doi:10.1016/j.fsigen.2017.01.017> and Vilsen et al. (2018) <doi:10.1016/j.fsigen.2018.04.003>. Note: that the parallelisation in the package relies on mclapply() and, thus, speed-ups will only be seen on UNIX based systems.
Authors:
STRMPS_0.6.9.tar.gz
STRMPS_0.6.9.zip(r-4.5)STRMPS_0.6.9.zip(r-4.4)STRMPS_0.5.8.zip(r-4.3)
STRMPS_0.6.9.tgz(r-4.5-any)STRMPS_0.6.9.tgz(r-4.4-any)
STRMPS_0.6.9.tar.gz(r-4.5-noble)STRMPS_0.6.9.tar.gz(r-4.4-noble)
STRMPS_0.6.9.tgz(r-4.4-emscripten)STRMPS_0.5.8.tgz(r-4.3-emscripten)
STRMPS.pdf |STRMPS.html✨
STRMPS/json (API)
# Install 'STRMPS' in R: |
install.packages('STRMPS', repos = c('https://svilsen.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/svilsen/strmps/issues
- flankingRegions - Flanking regions
- genotypeList - Genotype list
- identifiedSTRs - Identified STR regions
- noiseList - Noise list
- stringCoverageGenotypeList - Combined string coverage and genotype information
- stringCoverageList - Aggregated string coverage.
biostringspwalignshortreadiranges
Last updated 2 days agofrom:7d4955a23b. Checks:4 OK, 1 FAILURE, 3 ERROR. Indexed: yes.
Target | Result | Latest binary |
---|---|---|
Doc / Vignettes | OK | Mar 07 2025 |
R-4.5-win | ERROR | Mar 07 2025 |
R-4.5-mac | ERROR | Mar 07 2025 |
R-4.5-linux | ERROR | Mar 07 2025 |
R-4.4-win | OK | Mar 07 2025 |
R-4.4-mac | OK | Mar 07 2025 |
R-4.4-linux | OK | Mar 07 2025 |
R-4.3-win | OUTDATED | Dec 05 2024 |
Exports:BLMMfindNeighboursfindStuttergetGenotypeidentifyNoiseidentifySTRRegionsidentifySTRRegions.controlmergeGenotypeStringCoveragemergeNoiseStringCoveragephredQualityProbabilityphredQualityScoresolexaQualityProbabilitysolexaQualityScorestringCoveragestringCoverage.controlSTRMPSWorkflowSTRMPSWorkflowBatchSTRMPSWorkflowCollectStuttersworkflow.control
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopsclicodetoolscpp11crayoncurlDelayedArraydeldirdplyrfansiformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehttrhwriterinterpIRangesjpegjsonlitelambda.rlatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigpngpurrrpwalignR6RColorBrewerRcppRcppEigenRhtslibrlangRsamtoolsS4ArraysS4VectorsShortReadsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXVector