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")):
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("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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/staRgate/ |
| Package Short Url | https://bioconductor.org/packages/staRgate/ |
| Package Downloads Report | Download Stats |