Package: CytoPipelineGUI 1.5.0

Philippe Hauchamps

CytoPipelineGUI: GUI's for visualization of flow cytometry data analysis pipelines

This package is the companion of the `CytoPipeline` package. It provides GUI's (shiny apps) for the visualization of flow cytometry data analysis pipelines that are run with `CytoPipeline`. Two shiny applications are provided, i.e. an interactive flow frame assessment and comparison tool and an interactive scale transformations visualization and adjustment tool.

Authors:Philippe Hauchamps [aut, cre], Laurent Gatto [aut], Dan Lin [ctb]

CytoPipelineGUI_1.5.0.tar.gz
CytoPipelineGUI_1.5.0.zip(r-4.5)CytoPipelineGUI_1.5.0.zip(r-4.4)CytoPipelineGUI_1.3.0.zip(r-4.3)
CytoPipelineGUI_1.5.0.tgz(r-4.4-any)CytoPipelineGUI_1.3.0.tgz(r-4.3-any)
CytoPipelineGUI_1.5.0.tar.gz(r-4.5-noble)CytoPipelineGUI_1.5.0.tar.gz(r-4.4-noble)
CytoPipelineGUI_1.5.0.tgz(r-4.4-emscripten)CytoPipelineGUI_1.3.0.tgz(r-4.3-emscripten)
CytoPipelineGUI.pdf |CytoPipelineGUI.html✨
CytoPipelineGUI/json (API)
NEWS

# Install 'CytoPipelineGUI' in R:

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

Bug tracker:https://github.com/uclouvain-cbio/cytopipelinegui/issues

On BioConductor:CytoPipelineGUI-1.5.0(bioc 3.21)CytoPipelineGUI-1.4.0(bioc 3.20)

flowcytometry preprocessing qualitycontrol workflowstep immunooncology software visualization gui shinyapps

4.85 score 2 scripts 110 downloads 6 exports 138 dependencies

Last updated 23 days agofrom:d7627a815c. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 18 2024
R-4.5-win	NOTE	Nov 18 2024
R-4.5-linux	NOTE	Nov 18 2024
R-4.4-win	NOTE	Nov 18 2024
R-4.4-mac	NOTE	Nov 18 2024
R-4.3-win	NOTE	Sep 28 2024
R-4.3-mac	NOTE	Sep 28 2024

Exports:CytoPipelineCheckApp plotDiffFlowFrame plotScaleTransformedChannel plotSelectedFlowFrame plotSelectedWorkflow ScaleTransformApp

Dependencies:abind askpass base64enc BH Biobase BiocFileCache BiocGenerics BiocParallel bit bit64 blob bslib cachem changepoint circlize cli clue cluster codetools colorspace commonmark ComplexHeatmap cpp11 crayon crosstalk curl cytolib CytoPipeline data.table DBI dbplyr DelayedArray diagram digest doParallel dplyr evaluate fansi farver fastmap filelock flowAI flowCore flowWorkspace fontawesome foreach formatR fs futile.logger futile.options generics GetoptLong ggcyto ggplot2 GlobalOptions glue graph gridExtra gtable hexbin highr htmltools htmlwidgets httpuv httr IRanges isoband iterators jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell ncdfFlow nlme openssl PeacoQC pillar pkgconfig plogr plotly plyr png promises purrr R6 rappdirs RBGL RColorBrewer Rcpp reshape2 Rgraphviz Rhdf5lib rjson rlang rmarkdown RProtoBufLib RSQLite S4Arrays S4Vectors sass scales shape shiny snow sourcetools SparseArray stringi stringr sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun XML xtable XVector yaml zlibbioc zoo

CytoPipelineGUI : visualization of Flow Cytometry Data Analysis Pipelines run with CytoPipeline

Philippe Hauchamps, Laurent Gatto

Rendered fromCytoPipelineGUI.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2023-09-05
Started: 2023-07-04

Demonstration of the CytoPipeline R package suite functionalities

Philippe Hauchamps, Laurent Gatto

Rendered fromDemo.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2023-09-04
Started: 2023-09-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
interactive visualization of flow cytometry data analysis pipeline objects stored in cache	CytoPipelineCheckApp
Plot the difference plot between two flow frames from a CytoPipeline run	plotDiffFlowFrame
Plot a flow frame in 1D with explicit user given scale transform	plotScaleTransformedChannel
Plot a flow frame from a CytoPipeline run	plotSelectedFlowFrame
Plot a pipeline workflow from a CytoPipeline run	plotSelectedWorkflow
interactive display and modification of scale transform list	ScaleTransformApp