flowCut
This is the development version of flowCut; for the stable release version, see flowCut.
Automated Removal of Outlier Events and Flagging of Files Based on Time Versus Fluorescence Analysis
Bioconductor version: Development (3.24)
Common techinical complications such as clogging can result in spurious events and fluorescence intensity shifting, flowCut is designed to detect and remove technical artifacts from your data by removing segments that show statistical differences from other segments.
Author: Justin Meskas [cre, aut], Sherrie Wang [aut]
Maintainer: Justin Meskas <justinmeskas at gmail.com>
citation("flowCut")):
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("flowCut")
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("flowCut")| _**flowCut**_: Precise and Accurate Automated Removal of Outlier Events and Flagging of Files Based on Time Versus Fluorescence Analysis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CellBasedAssays, FlowCytometry, Preprocessing, QualityControl, Software |
| Version | 1.23.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.4), flowCore |
| Imports | flowDensity(>= 1.13.1), Cairo, e1071, grDevices, graphics, stats, methods |
| System Requirements | |
| URL |
See More
| Suggests | RUnit, BiocGenerics, knitr, markdown, rmarkdown |
| 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 | flowCut_1.23.0.tar.gz |
| Windows Binary (x86_64) | flowCut_1.23.0.zip |
| macOS Binary (big-sur-x86_64) | flowCut_1.23.0.tgz |
| macOS Binary (sonoma-arm64) | flowCut_1.23.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/flowCut |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/flowCut |
| Bioc Package Browser | https://code.bioconductor.org/browse/flowCut/ |
| Package Short Url | https://bioconductor.org/packages/flowCut/ |
| Package Downloads Report | Download Stats |