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strvalidator

STR-validator is a free and open source R-package intended for process control and internal validation of forensic STR DNA typing kit. Its graphical user interface simplifies the analysis of data exported from e.g. GeneMapper software, without extensive knowledge about R. It provides functions to import, view, edit, and export data. After analysis the results, generated plots, heat-maps, and data can be saved in a project for easy access. Currently, analysis modules for stutter, balance, dropout, mixture, concordance, typing result, precision, pull-up, and analytical thresholds are available. In addition there are functions to analyse the GeneMapper bins- and panels files. EPG like plots can be generate from data. STR-validator can greatly increase the speed of validation by reducing the time and effort needed to analyse the validation data. It allows exploration of the characteristics of DNA typing kits according to ENFSI and SWGDAM recommendations. This facilitates the implementation of probabilistic interpretation of DNA results.

STR-validator is written and maintained by Oskar Hansson, senior forensic scientist at the Norwegian Institute of Public Health (NIPH), Department of Forensic Biology. The work has received external funding from the European Union seventh Framework Programme (FP7/2007-2013) under grant agreement no 285487 (EUROFORGEN-NoE) but development and maintenance is now performed as a part of my position at NIPH, and on personal spare time.

More information can be found at: https://sites.google.com/site/forensicapps/strvalidator

Info and user community at Facebook: https://www.facebook.com/pages/STR-validator/240891279451450?ref=tn_tnmn https://www.facebook.com/groups/strvalidator/

The source code is hosted at GitHub: https://github.com/OskarHansson/strvalidator

Please report bugs to: https://github.com/OskarHansson/strvalidator/issues

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Version

Install

install.packages('strvalidator')

Monthly Downloads

274

Version

1.7.0

License

GPL-2

Maintainer

Last Published

July 5th, 2016

Functions in strvalidator (1.7.0)

addData_gui

Add Data
addColor

Add Color Information.
addDye_gui

Add Dye Information
addMarker_gui

Add Missing Markers
addSize_gui

Add Size Information
addMarker

Add Missing Markers.
calculateAllele

Calculate Allele
calculateAllele_gui

Calculate Allele
addData

Adds New Data Columns to a Data Frame
addSize

Add Size Information.
calculateAT_gui

Calculate Analytical Threshold
calculateCapillary

Calculate Capillary Balance
calculateConcordance

Calculate Concordance.
calculateBalance_gui

Calculate Balance
calculateConcordance_gui

Calculate Concordance
calculateBalance

Calculate Balance
calculateAT6

Calculate Analytical Threshold
calculateAT6_gui

Calculate Analytical Threshold
calculateAT

Calculate Analytical Threshold
calculateCapillary_gui

Calculate Capillary Balance
calculateMixture_gui

Calculate Mixture
calculateDropout_gui

Calculate Dropout Events
calculateHeterozygous

Calculate Heterozygous Loci
calculateHeight

Calculate Peak Height.
calculateHeterozygous_gui

Calculate Heterozygous Loci
calculateLb_gui

Calculate Locus Balance
calculateLb

Calculate Inter-locus Balance
calculateDropout

Calculate Drop-out Events
calculateHeight_gui

Calculate Peak Height
calculateMixture

Calculate Mixture.
calculatePeaks_gui

Calculate Peaks
calculateOL_gui

Analyse Off-ladder Alleles
calculateRatio_gui

Calculate Ratio
calculatePullup_gui

Calculate Spectral Pull-up
calculateOL

Analyse Off-ladder Alleles
calculatePeaks

Calculate Peaks
calculateOverlap_gui

Calculate Bins Overlap
calculatePullup

Calculate Spectral Pull-up
calculateOverlap

Calculate Bins Overlap
calculateRatio

Calculate Ratio
calculateSlope

Calculate Profile Slope.
calculateSlope_gui

Calculate Profile Slope
calculateStutter

Calculate Stutter
checkDataset

Check Dataset
calculateStutter_gui

Calculate Stutter
calculateResultType_gui

Calculate Result Type
calculateResultType

Calculate Result Type
checkSubset_gui

Check Subset
calculateSpike_gui

Detect Spike
calculateSpike

Detect Spike
combine_gui

Combine Datasets
filterProfile_gui

Filter Profile
filterProfile

Filter Profile
columns

Column Actions
import_gui

Import Data
plotSlope_gui

Plot Profile Slope
plotResultType_gui

Plot Result Type
import

Import Data
ref51

ESX17 example data for mixture analysis.
ref52

ESX17 example data for mixture analysis.
guessProfile_gui

Guess Profile
ggsave_gui

Save Image
cropData_gui

Crop Or Replace
combineBinsAndPanels

Combine Bins And Panels Files.
listObjects

List Objects
plotKit_gui

Plot Kit Marker Ranges
plotDropout_gui

Plot Drop-out Events
makeKit_gui

Make Kit
ref11

ESX17 Positive Control Profile
colNames

Column Names
plotAT_gui

Plot Analytical Threshold
export_gui

Export
columns_gui

Column Actions
export

Export
set5

ESX17 example data for mixture analysis.
plotCapillary_gui

Plot Capillary Balance
guessProfile

Guess Profile
heightToPeak

Height To Peak.
plotDistribution_gui

Plot Distribution
plotStutter_gui

Plot Stutter
removeArtefact

Remove Artefacts
removeArtefact_gui

Remove Artefact
set3

ESX17 example data for dropout analysis.
strvalidator-package

Process Control and Internal Validation of Forensic STR Kits
ref2

SGMPlus example data
strvalidator

Graphical User Interface For The STR-validator Package
set4

ESX17 example data for dropout analysis.
trim_gui

Trim Data
trim

Trim Data
checkSubset

Check Subset
colConvert

Convert Columns
plotPeaks_gui

Plot Peaks
getKit

Get Kit
getDb

Get Allele Frequency Database
removeSpike

Remove Spikes
plotPrecision_gui

Plot Precision
ref1

ESX17 Positive Control Profile
readPanelsFile

Read Panels File
plotBalance_gui

Plot Balance
slim_gui

Slim Data Frames
saveObject

Save Object
tableCapillary_gui

Table Capillary
scrambleAlleles

Scramble Alleles
tableCapillary

Table Capillary
generateEPG

Generate EPG
detectKit

Detect Kit
maskAT

Mask And Prepare Data To Analyze Analytical Threshold
generateEPG_gui

Generate EPG
modelDropout_gui

Model And Plot Drop-out Events
plotPullup_gui

Plot Pull-up
plotRatio_gui

Plot Ratio
readBinsFile

Read Bins file
ref4

ESX17 example data for dropout analysis.
ref3

ESX17 example data for dropout analysis.
slim

Slim Data Frames
set2

SGMPlus example data
tableStutter_gui

Table Stutter
sortMarker

Sort Markers
tableStutter

Table Stutter
removeSpike_gui

Remove Spike
tableBalance_gui

Table Balance
editData_gui

Edit or View Data Frames
tableBalance

Table Balance
tablePrecision

Calculate Precision
set1

Typing data in 'GeneMapper' format
tablePrecision_gui

Table Precision