staRgate
This is the development version of staRgate; for the stable release version, see staRgate.
Automated gating pipeline for flow cytometry analysis to characterize the lineage, differentiation, and functional states of T-cells
Bioconductor version: Development (3.24)
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.
Author: Jasme Lee [aut, cre] 
, 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]
Maintainer: Jasme Lee <leej22 at mskcc.org>
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 1.1.0, https://bioconductor.org/packages/staRgate.
Generated from the package metadata; it may differ from the package's own citation.
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("staRgate")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("staRgate")| Tutorial: Running the pipeline | HTML | R Script |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | FlowCytometry, ImmunoOncology, Preprocessing, Software |
| Version | 1.1.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.3.0) |
| Imports | dplyr, janitor, purrr, rlang, stringr, tidyr, flowCore, flowWorkspace, glue, tibble |
| System Requirements | |
| URL | https://bioconductor.org/packages/staRgate https://leejasme.github.io/staRgate |
| Bug Reports | https://github.com/leejasme/staRgate/issues |
See More
| Suggests | flowAI, ggplot2, gt, knitr, openCyto, ggcyto, rmarkdown, data.table, here, testthat (>= 3.0.0), BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | staRgate_1.1.0.tar.gz |
| Windows Binary (x86_64) | staRgate_1.1.0.zip |
| macOS Binary (big-sur-x86_64) | staRgate_1.1.0.tgz |
| macOS Binary (sonoma-arm64) | staRgate_1.1.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/staRgate |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/staRgate |
| Package Short Url | https://bioconductor.org/packages/staRgate/ |
| Package Downloads Report | Download Stats |