Introduction | Installation | Reading profiles | Alleles are stored pre-split | Marker names | Metadata | Scoring | Comparing end to end | Mixing | Writing results | Querying Cellosaurus | The command line application | The Shiny application | STRprofilerR in a larger workflow | Bioconductor data structures | The bundled PDX database | Generating profiles from raw data | Carrying authentication info with an experiment | Maintaining a reference database | Session info
Package: STRprofilerR 0.99.1
Jared Andrews
STRprofilerR: Compare Short Tandem Repeat Profiles for Model Authentication
Compares short tandem repeat (STR) profiles to authenticate biomedical models such as cell lines and xenografts against the primary tissue samples they were derived from. Provides the Tanabe (Sorenson-Dice), Masters (versus query), and Masters (versus reference) similarity scores, heuristics for detecting sample mixing, flexible ingest of wide and long profile formats, comparison against user-supplied reference databases, and querying of the Cellosaurus knowledge base through the CLASTR REST API. A command line application is included for use in automated workflows, and a Shiny application for interactive queries.
Authors:
STRprofilerR_0.99.1.tar.gz
STRprofilerR_0.99.1.zip(r-4.7-any)STRprofilerR_0.99.1.zip(r-4.6-any)STRprofilerR_0.99.1.zip(r-4.5-any)
STRprofilerR_0.99.1.tgz(r-4.6-any)STRprofilerR_0.99.1.tgz(r-4.5-any)
STRprofilerR_0.99.1.tar.gz(r-4.7-any)STRprofilerR_0.99.1.tar.gz(r-4.6-any)
STRprofilerR_0.99.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
STRprofilerR/json (API)
| # Install 'STRprofilerR' in R: |
| install.packages('STRprofilerR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/j-andrews7/strprofilerr/issues
Datasets:
- pdxSTRProfiles - STR profiles of patient-derived models from JAX and the NCI PDMR
softwarequalitycontrolgeneticscellbasedassayscell-line-authenticationmodel-authenticationomnistrpowerplexstr-profilingxenograft-authentication
Last updated from:fa9daea6b9. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 354 | ||
| linux-devel | OK | 252 | ||
| source / vignettes | OK | 334 | ||
| linux-release | OK | 449 | ||
| macos-release | OK | 166 | ||
| macos-oldrel | OK | 149 | ||
| windows-devel | OK | 156 | ||
| windows-release | OK | 333 | ||
| windows-oldrel | OK | 155 | ||
| wasm-release | OK | 274 |
Exports:allelesalleles<-amelogeninMarkersas.data.frameclassifyMarkersclastrBatchQueryclastrMarkersclastrQuerycleanAllelescompareProfilesflagMixedSamplesharmonizeMarkersmarkerAliasesmarkerDatamarkerData<-markersparamsprovenancequeryProfilesreadSTRProfilesreferenceProfilessampleDatasampleData<-scoreProfilesscoreQueryscoresshowstrHTMLTableSTRprofilerAppSTRProfilessummarizeMatchessummaryvalidateClastrMarkerswriteSTRProfileswriteSTRResults
Dependencies:askpassBiocGenericsclicurlgenericsgluehttr2IRangeslatticelifecyclemagrittrMatrixopensslR6rlangS4Vectorssysvctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Accessors for STRProfiles objects | alleles alleles,STRProfiles-method alleles<- alleles<-,STRProfiles-method markerData markerData,STRProfiles-method markerData<- markerData<-,STRProfiles-method markers markers,STRProfiles-method provenance provenance,STRProfiles-method sampleData sampleData,STRProfiles-method sampleData<- sampleData<-,STRProfiles-method STRProfiles-accessors |
| Recognised amelogenin marker names | amelogeninMarkers |
| Classify STR markers | classifyMarkers |
| Query CLASTR in batch and save the XLSX result | clastrBatchQuery |
| Marker names accepted by the CLASTR API | clastrMarkers validateClastrMarkers |
| Query the Cellosaurus knowledge base via CLASTR | clastrQuery |
| Clean and split a vector of allele calls | cleanAlleles |
| Compare STR profiles end to end | compareProfiles |
| Flag potentially mixed samples | flagMixedSamples |
| Marker name harmonisation | harmonizeMarkers markerAliases |
| STR profiles of patient-derived models from JAX and the NCI PDMR | pdxSTRProfiles |
| Read STR profiles from file | readSTRProfiles |
| Score STR profiles against each other | scoreProfiles |
| Score a single profile against a reference set | scoreQuery |
| Accessors for STRComparison objects | params params,STRComparison-method queryProfiles queryProfiles,STRComparison-method referenceProfiles referenceProfiles,STRComparison-method scores scores,STRComparison-method show,STRComparison-method STRComparison-accessors summary,STRComparison-method |
| STRComparison: the result of comparing STR profiles | STRComparison STRComparison-class |
| Write a data frame as a standalone HTML table | strHTMLTable |
| Launch the STRprofiler Shiny application | STRprofilerApp |
| Build STRProfiles from a data.frame | STRProfiles |
| STRProfiles: a set of short tandem repeat profiles | STRProfiles-class |
| Dimensions, subsetting, and coercion for STRProfiles | $,STRProfiles-method as.data.frame,STRProfiles-method c,STRProfiles-method dim,STRProfiles-method dimnames,STRProfiles-method show,STRProfiles-method STRProfiles-methods [,STRProfiles,ANY,ANY,ANY-method [,STRProfiles-method |
| Summarise pairwise scores into one row per query | summarizeMatches |
| Write STR profiles to file | writeSTRProfiles |
| Write comparison results to disk | writeSTRResults |