flowGate
This is the development version of flowGate; for the stable release version, see flowGate.
Interactive Cytometry Gating in R
Bioconductor version: Development (3.24)
flowGate adds an interactive Shiny app to allow manual GUI-based gating of flow cytometry data in R. Using flowGate, you can draw 1D and 2D span/rectangle gates, quadrant gates, and polygon gates on flow cytometry data by interactively drawing the gates on a plot of your data, rather than by specifying gate coordinates. This package is especially geared toward wet-lab cytometerists looking to take advantage of R for cytometry analysis, without necessarily having a lot of R experience.
Author: Andrew Wight [aut, cre]
, Harvey Cantor [aut, ldr]
Maintainer: Andrew Wight <andrew.wight10 at gmail.com>
citation("flowGate")):
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("flowGate")
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("flowGate")| flowGate | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, FlowCytometry, ImmunoOncology, Preprocessing, Software, WorkflowStep |
| Version | 1.13.1 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 years) |
| License | MIT + file LICENSE |
| Depends | flowWorkspace(>= 4.0.6), ggcyto(>= 1.16.0), R (>= 4.4) |
| Imports | shiny (>= 1.5.0), BiocManager (>= 1.30.10), flowCore(>= 2.0.1), dplyr (>= 1.0.0), ggplot2 (>= 3.3.2), rlang (>= 0.4.7), purrr, tibble, methods, openCyto, stringr |
| System Requirements | |
| URL | https://www.bioconductor.org/packages/release/bioc/html/flowGate.html |
| Bug Reports | https://github.com/NKInstinct/flowGate/issues |
See More
| Suggests | knitr, rmarkdown, tidyverse, testthat, vdiffr |
| 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 | flowGate_1.13.1.tar.gz |
| Windows Binary (x86_64) | flowGate_1.13.1.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | flowGate_1.13.1.tgz |
| macOS Binary (sonoma-arm64) | flowGate_1.13.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/flowGate |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/flowGate |
| Bioc Package Browser | https://code.bioconductor.org/browse/flowGate/ |
| Package Short Url | https://bioconductor.org/packages/flowGate/ |
| Package Downloads Report | Download Stats |