Package: CyFj11 0.99.113

Bernd Jagla

CyFj11: Parse FlowJo V11 Workspace Files and Export to FlowJo V10

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.

Authors:Bernd Jagla [aut, cre], Slobodan Culina [aut], Francois Le Guerroue [aut], Esma Karkeni [aut], Milena Hasan [aut]

CyFj11_0.99.113.tar.gz
CyFj11_0.99.113.zip(r-4.7-any)CyFj11_0.99.113.zip(r-4.6-any)CyFj11_0.99.113.zip(r-4.5-any)
CyFj11_0.99.113.tgz(r-4.6-any)CyFj11_0.99.113.tgz(r-4.5-any)
CyFj11_0.99.113.tar.gz(r-4.7-any)CyFj11_0.99.113.tar.gz(r-4.6-any)
CyFj11_0.99.113.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CyFj11/json (API)

# Install 'CyFj11' in R:

install.packages('CyFj11', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/c3bi-pasteur-fr/cyfj11/issues

On CRAN:

flowcytometry dataimport infrastructure preprocessing

3.98 score 9 exports 70 dependencies

Last updated from:ab0d40a4fc. Checks:10 OK. Indexed: yes.

Target	Result	Time
bioc-checks	OK	196
linux-devel	OK	371
source / vignettes	OK	271
linux-release	OK	280
macos-release	OK	201
macos-oldrel	OK	173
windows-devel	OK	219
windows-release	OK	308
windows-oldrel	OK	221
wasm-release	OK	160

Exports:export_flowjo10_workspace fj11_to_gatingset get_sanitize_slashes get_verbose load_example_workspace pretty_print_flowjo read_flowjo11_workspace set_sanitize_slashes set_verbose

Dependencies:abind BH Biobase BiocGenerics biocmake bit bit64 cli clipr cpp11 crayon cytolib data.table DelayedArray dir.expiry dplyr farver filelock flowCore flowWorkspace generics ggplot2 glue graph gtable hms IRanges isoband jsonlite labeling lattice lifecycle magrittr Matrix MatrixGenerics matrixStats ncdfFlow pillar pkgconfig prettyunits progress purrr R6 RBGL RColorBrewer Rcpp readr Rgraphviz Rhdf5lib rlang RProtoBufLib S4Arrays S4Vectors S7 scales SparseArray stringi stringr tibble tidyr tidyselect tzdb utf8 vctrs viridisLite vroom withr XML xml2 XVector

Getting Started with CyFj11

Rendered fromgetting-started.Rmdusingknitr::rmarkdown

Last update: 2026-09-14
Started: 2026-03-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Export GatingSet to FlowJo v10 Workspace	export_flowjo10_workspace
Convert FlowJo v11 Workspace to GatingSet	fj11_to_gatingset
Get slash sanitization mode	get_sanitize_slashes
Get verbose mode	get_verbose
Load Example FlowJo v11 Workspace	load_example_workspace
Pretty Print FlowJo Workspace	pretty_print_flowjo
Read FlowJo v11 Workspace	read_flowjo11_workspace
Set parameter name slash sanitization behavior	set_sanitize_slashes
Set verbose mode	set_verbose