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STRMPS  

Analysis of Short Tandem Repeat (STR) Massively Parallel Sequencing (MPS) Data
View on CRAN: Click here


Download and install STRMPS package within the R console
Install from CRAN:
install.packages("STRMPS")

Install from Github:
library("remotes")
install_github("cran/STRMPS")

Install by package version:
library("remotes")
install_version("STRMPS", "0.6.8")



Attach the package and use:
library("STRMPS")
Maintained by
Søren B. Vilsen
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-07-02
Latest Update: 2018-07-02
Description:
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.
How to cite:
Søren B. Vilsen (2018). STRMPS: Analysis of Short Tandem Repeat (STR) Massively Parallel Sequencing (MPS) Data. R package version 0.6.8, https://cran.r-project.org/web/packages/STRMPS. Accessed 29 Mar. 2025.
Previous versions and publish date:
0.5.8 (2018-07-02 10:30), 0.6.8 (2025-02-22 01:20)
Other packages that cited STRMPS R package
View STRMPS citation profile
Other R packages that STRMPS depends, imports, suggests or enhances
Complete documentation for STRMPS
Functions, R codes and Examples using the STRMPS R package
Some associated functions: BLMM . STRMPSWorkflow . STRMPSWorkflowBatch . STRMPSWorkflowCollectStutters . extractedReadsList-class . extractedReadsListCombined-class . extractedReadsListNonCombined-class . extractedReadsListReverseComplement-class . findNeighbours-stringCoverageGenotypeList-method . findNeighbours . findStutter-stringCoverageGenotypeList-method . findStutter . flankingRegions . genotypeIdentifiedList-class . genotypeList . getGenotype-stringCoverageList-method . getGenotype . identifiedSTRs . identifyNoise-stringCoverageList-method . identifyNoise . identifySTRRegions-ShortReadQ-method . identifySTRRegions-character-method . identifySTRRegions.control . identifySTRRegions . mergeGenotypeStringCoverage-genotypeIdentifiedList-method . mergeGenotypeStringCoverage . mergeNoiseStringCoverage-noiseIdentifiedList-method . mergeNoiseStringCoverage . neighbourList-class . noiseIdentifiedList-class . noiseList . probabilityOfError . qualityScore . stringCoverage-extractedReadsList-method . stringCoverage-extractedReadsListCombined-method . stringCoverage-extractedReadsListNonCombined-method . stringCoverage-extractedReadsListReverseComplement-method . stringCoverage.control . stringCoverage . stringCoverageGenotypeList-class . stringCoverageGenotypeList . stringCoverageList-class . stringCoverageList . stringCoverageNoiseList-class . workflow.control . 
Some associated R codes: STR_Region_Identification.R . all_in_one_workflow_fun.R . allele_genotype_functions.R . auxiliary_functions.R . quality_functions.R . stutter_functions.R .  Full STRMPS package functions and examples
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