staRgate
Automated gating pipeline for flow cytometry analysis to characterize the lineage, differentiation, and functional states of T-cells
Bioconductor version: 3.23 · Package version: 1.0.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
An R-based automated gating pipeline for flow cytometry data designed to mimic the manual gating strategy of defining flow biomarker positive populations relative to a unimodal background population to include cells with varying intensities of marker expression. The pipeline’s main feature is a flexible density-based gating strategy capable of capturing varying scenarios based on marker expression patterns to analyze a 29-marker flow panel that characterizes T-cell lineage, differentiation, and functional states.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("staRgate")Details
| Maintainer | Jasme Lee <leej22@mskcc.org> |
| Author | Jasme Lee [aut, cre] (ORCID: <https://orcid.org/0009-0006-4492-4872>), Matthew Adamow [aut], Colleen Maher [aut], Xiyu Peng [aut], Phillip Wong [aut], Fiona Ehrich [aut], Michael A Postow [aut], Margaret K Callahan [aut], Ronglai Shen [aut], Katherine S Panageas [aut], V foundation [fnd], MSK-MIND [fnd], NIH R01CA276286 [fnd], NIH P30CA008748 [fnd] |
| License | MIT + file LICENSE |
| URL | https://bioconductor.org/packages/staRgate, https://leejasme.github.io/staRgate |
| Bug Reports | https://github.com/leejasme/staRgate/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | FlowCytometry, ImmunoOncology, Preprocessing, Software |
| Package Short Url | https://bioconductor.org/packages/staRgate/ |
Citation
From within R, enter citation("staRgate"):
Jasme Lee, Matthew Adamow, Colleen Maher, Xiyu Peng, Phillip Wong, Fiona Ehrich, Michael A Postow, Margaret K Callahan, Ronglai Shen, Katherine S Panageas. staRgate: Automated gating pipeline for flow cytometry analysis to characterize the lineage, differentiation, and functional states of T-cells. doi:10.18129/B9.bioc.staRgate, R package version 1.0.0, https://bioconductor.org/packages/staRgate.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | staRgate_1.0.0.tar.gz |
| Windows binary (x86_64) | staRgate_1.0.0.zip |
| macOS binary (arm64) | staRgate_1.0.0.tgz |
| macOS binary (x86_64) | staRgate_1.0.0.tgz |