STRprofilerR
This is the development version of STRprofilerR; to use it, please install the devel version of Bioconductor.
Compare Short Tandem Repeat Profiles for Model Authentication
Bioconductor version: Development (3.24)
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.
Author: Jared Andrews [aut, cre]
Maintainer: Jared Andrews <jared.andrews07 at gmail.com>
citation("STRprofilerR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("STRprofilerR")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("STRprofilerR")| Comparing STR profiles with STRprofilerR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CellBasedAssays, Genetics, QualityControl, Software |
| Version | 0.99.1 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0) |
| Imports | httr2, IRanges, Matrix, methods, S4Vectors, stats, tools, utils |
| System Requirements | |
| URL | https://github.com/j-andrews7/STRprofilerR |
| Bug Reports | https://github.com/j-andrews7/STRprofilerR/issues |
See More
| Suggests | BiocStyle, bslib (>= 0.7.0), curl, DT, htmlwidgets, jsonlite, knitr, Rapp, readxl, rmarkdown, shiny (>= 1.8.1), SummarizedExperiment, testthat (>= 3.0.0), withr, writexl |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | STRprofilerR_0.99.1.tar.gz |
| Windows Binary (x86_64) | STRprofilerR_0.99.1.zip |
| macOS Binary (big-sur-x86_64) | STRprofilerR_0.99.1.tgz |
| macOS Binary (sonoma-arm64) | STRprofilerR_0.99.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/STRprofilerR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/STRprofilerR |
| Bioc Package Browser | https://code.bioconductor.org/browse/STRprofilerR/ |
| Package Short Url | https://bioconductor.org/packages/STRprofilerR/ |
| Package Downloads Report | Download Stats |