CyFj11
This is the development version of CyFj11; to use it, please install the devel version of Bioconductor.
Parse FlowJo V11 Workspace Files and Export to FlowJo V10
Bioconductor version: Development (3.24)
Provides functions to parse FlowJo v11 workspace files (.flowjo) and extract gating information, populations, and associated FCS files. Includes utilities for exporting data to FlowJo v10 workspace format. The package enables bidirectional data flow between FlowJo and R/Bioconductor, facilitating reproducible analysis workflows.
Author: Bernd Jagla [aut, cre] (ORCID:
, affiliation: Institut Pasteur, scBiomarkers UTechS & Bioinformatics & Biostatistics Hub), Slobodan Culina [aut] (affiliation: Institut Pasteur, scBiomarkers UTechS), Francois Le Guerroue [aut] (affiliation: Institut Pasteur, scBiomarkers UTechS), Esma Karkeni [aut] (affiliation: Institut Pasteur, scBiomarkers UTechS), Milena Hasan [aut] (affiliation: Institut Pasteur, scBiomarkers UTechS)
Maintainer: Bernd Jagla <bernd.jagla at pasteur.fr>
citation("CyFj11")):
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("CyFj11")
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("CyFj11")| Getting Started with CyFj11 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, FlowCytometry, Infrastructure, Preprocessing, Software |
| Version | 0.99.113 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0) |
| Imports | jsonlite, dplyr, flowWorkspace, flowCore, readr, rlang, tibble, tidyr, xml2, methods, scales, magrittr, stats, utils |
| System Requirements | |
| URL | https://github.com/C3BI-pasteur-fr/CyFj11 |
| Bug Reports | https://github.com/C3BI-pasteur-fr/CyFj11/issues |
See More
| Suggests | testthat (>= 3.0.0), Biobase, CytoML, FlowSOM, flowWorkspaceData, ggcyto, knitr, mockery, BiocStyle, qpdf, 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 | CyFj11_0.99.113.tar.gz |
| Windows Binary (x86_64) | CyFj11_0.99.113.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | CyFj11_0.99.113.tgz |
| macOS Binary (sonoma-arm64) | CyFj11_0.99.113.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CyFj11 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CyFj11 |
| Bioc Package Browser | https://code.bioconductor.org/browse/CyFj11/ |
| Package Short Url | https://bioconductor.org/packages/CyFj11/ |
| Package Downloads Report | Download Stats |