staRgate
This is the development version of staRgate; to use it, please install the devel version of Bioconductor.
Automated gating pipeline for flow cytometry analysis to characterize the lineage, differentiation, and functional states of T-cells
Bioconductor version: Development (3.23)
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.
Maintainer: Jasme Lee <leej22 at mskcc.org>
citation("staRgate")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
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 |
Details
| biocViews | FlowCytometry, ImmunoOncology, Preprocessing, Software |
| Version | 0.99.4 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | dplyr, janitor, purrr, rlang, stringr, tidyr, flowCore, flowWorkspace, glue, tibble |
| System Requirements | |
| URL | https://leejasme.github.io/staRgate/ https://github.com/leejasme/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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | staRgate_0.99.4.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | staRgate_0.99.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/staRgate |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/staRgate |
| Bioc Package Browser | https://code.bioconductor.org/browse/staRgate/ |
| Package Short Url | https://bioconductor.org/packages/staRgate/ |
| Package Downloads Report | Download Stats |