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:Søren B. Vilsen

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'))

Peer review:

Bug tracker:https://github.com/svilsen/strmps/issues

Datasets:

On CRAN:

biostringsshortreadiranges

2.00 score 110 downloads 19 exports 73 dependencies

Last updated 6 years agofrom:4d43819da5. Checks:OK: 1 NOTE: 5 WARNING: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 05 2024
R-4.5-winNOTENov 05 2024
R-4.5-linuxWARNINGNov 05 2024
R-4.4-winNOTENov 05 2024
R-4.4-macNOTENov 05 2024
R-4.3-winNOTENov 05 2024
R-4.3-macNOTEOct 06 2024

Exports:BLMMfindNeighboursfindStuttergetGenotypeidentifyNoiseidentifySTRRegionsidentifySTRRegions.controlmergeGenotypeStringCoveragemergeNoiseStringCoveragephredQualityProbabilityphredQualityScoresolexaQualityProbabilitysolexaQualityScorestringCoveragestringCoverage.controlSTRMPSWorkflowSTRMPSWorkflowBatchSTRMPSWorkflowCollectStuttersworkflow.control

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopsclicodetoolscpp11crayoncurlDelayedArraydeldirdplyrfansiformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehttrhwriterinterpIRangesjpegjsonlitelambda.rlatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigpngpurrrpwalignR6RColorBrewerRcppRcppEigenRhtslibrlangRsamtoolsS4ArraysS4VectorsShortReadsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXVectorzlibbioc

Readme and manuals

Help Manual

Help pageTopics
Block length of the missing motif.BLMM
Extract STR region informationextractedReadsList-class
Combined extract STR region information.extractedReadsListCombined-class
Combined extract STR region information.extractedReadsListNonCombined-class
Extract STR region information of the reverse complement DNA strand.extractedReadsListReverseComplement-class
Find neighboursfindNeighbours
Find neighboursfindNeighbours,stringCoverageGenotypeList-method
Find stuttersfindStutter
Find stuttersfindStutter,stringCoverageGenotypeList-method
Flanking regionsflankingRegions
Genotype listgenotypeIdentifiedList-class
Genotype listgenotypeList
Assigns genotype.getGenotype
Assigns genotype.getGenotype,stringCoverageList-method
Identified STR regionsidentifiedSTRs
Idenfities the noise.identifyNoise
Idenfities the noise.identifyNoise,stringCoverageList-method
Identify the STR regions of a fastq-file or ShortReadQ-object.identifySTRRegions
Identify the STR regions of a fastq-file or ShortReadQ-object.identifySTRRegions,character-method
Identify the STR regions of a fastq-file or ShortReadQ-object.identifySTRRegions,ShortReadQ-method
Control function for identifySTRRegionsidentifySTRRegions.control
Merge genotypeIdentifiedList and stringCoverageList.mergeGenotypeStringCoverage
Merge genotypeIdentifiedList and stringCoverageList.mergeGenotypeStringCoverage,genotypeIdentifiedList-method
Merge noiseIdentifiedList and stringCoverageList.mergeNoiseStringCoverage
Merge noiseIdentifiedList and stringCoverageList.mergeNoiseStringCoverage,noiseIdentifiedList-method
A neighbour listneighbourList-class
Noise listnoiseIdentifiedList-class
Noise listnoiseList
Quality score to probabilityphredQualityProbability solexaQualityProbability
Convert probability to quality scorephredQualityScore solexaQualityScore
Get string coverage STR identified objects.stringCoverage
Get string coverage STR identified objects.stringCoverage,extractedReadsList-method
Get string coverage STR identified objects.stringCoverage,extractedReadsListCombined-method
Get string coverage STR identified objects.stringCoverage,extractedReadsListNonCombined-method
Get string coverage STR identified objects.stringCoverage,extractedReadsListReverseComplement-method
String coverage coontrol objectstringCoverage.control
Combined string coverage and genotype informationstringCoverageGenotypeList
Combined stringCoverage- and genotypeIdentifiedListstringCoverageGenotypeList-class
Aggregated string coverage.stringCoverageList
A string coverage liststringCoverageList-class
Combined stringCoverage- and noiseIdentifiedListstringCoverageNoiseList-class
Workflow functionSTRMPSWorkflow
Batch wrapper for the workflow functionSTRMPSWorkflowBatch
Collect stutters filesSTRMPSWorkflowCollectStutters
Workflow default optionsworkflow.control