Package: STRMPS 0.5.8
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. 'STRMPS' can work with the package 'STRaitRazoR' (an R interface to the 'STRaitRazor' commandline tool) for added speed. 'STRaitRazoR' only works on linux and can found at <https://github.com/svilsen/STRaitRazoR>. 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>. Lastly, note that the parallelisation in the package relies on 'mclapply()' and, thus, speed-ups will only be seen on UNIX based systems.
Authors:
STRMPS_0.5.8.tar.gz
STRMPS_0.5.8.zip(r-4.5)STRMPS_0.5.8.zip(r-4.4)STRMPS_0.5.8.zip(r-4.3)
STRMPS_0.5.8.tgz(r-4.4-any)STRMPS_0.5.8.tgz(r-4.3-any)
STRMPS_0.5.8.tar.gz(r-4.5-noble)STRMPS_0.5.8.tar.gz(r-4.4-noble)
STRMPS_0.5.8.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.
Last updated 6 years agofrom:4d43819da5. Checks:OK: 1 WARNING: 1 NOTE: 5. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 05 2024 |
R-4.5-win | NOTE | Nov 05 2024 |
R-4.5-linux | WARNING | Nov 05 2024 |
R-4.4-win | NOTE | Nov 05 2024 |
R-4.4-mac | NOTE | Nov 05 2024 |
R-4.3-win | NOTE | Nov 05 2024 |
R-4.3-mac | NOTE | Oct 06 2024 |
Exports:BLMMfindNeighboursfindStuttergetGenotypeidentifyNoiseidentifySTRRegionsidentifySTRRegions.controlmergeGenotypeStringCoveragemergeNoiseStringCoveragephredQualityProbabilityphredQualityScoresolexaQualityProbabilitysolexaQualityScorestringCoveragestringCoverage.controlSTRMPSWorkflowSTRMPSWorkflowBatchSTRMPSWorkflowCollectStuttersworkflow.control
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopsclicodetoolscpp11crayoncurlDelayedArraydeldirdplyrfansiformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehttrhwriterinterpIRangesjpegjsonlitelambda.rlatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigpngpurrrpwalignR6RColorBrewerRcppRcppEigenRhtslibrlangRsamtoolsS4ArraysS4VectorsShortReadsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXVectorzlibbioc