Package: tidyFlowCore 1.7.0

Timothy Keyes

tidyFlowCore: tidyFlowCore: Bringing flowCore to the tidyverse

tidyFlowCore bridges the gap between flow cytometry analysis using the flowCore Bioconductor package and the tidy data principles advocated by the tidyverse. It provides a suite of dplyr-, ggplot2-, and tidyr-like verbs specifically designed for working with flowFrame and flowSet objects as if they were tibbles; however, your data remain flowCore data structures under this layer of abstraction. tidyFlowCore enables intuitive and streamlined analysis workflows that can leverage both the Bioconductor and tidyverse ecosystems for cytometry data.

Authors:Timothy Keyes [cre], Kara Davis [rth, own], Garry Nolan [rth, own]

tidyFlowCore_1.7.0.tar.gz
tidyFlowCore_1.7.0.zip(r-4.7)tidyFlowCore_1.7.0.zip(r-4.6)tidyFlowCore_1.7.0.zip(r-4.5)
tidyFlowCore_1.7.0.tgz(r-4.6-any)tidyFlowCore_1.7.0.tgz(r-4.5-any)
tidyFlowCore_1.7.0.tar.gz(r-4.7-any)tidyFlowCore_1.7.0.tar.gz(r-4.6-any)
tidyFlowCore_1.7.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
tidyFlowCore/json (API)

# Install 'tidyFlowCore' in R:

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

Bug tracker:https://github.com/keyes-timothy/tidyflowcore/issues

Pkgdown/docs site:https://keyes-timothy.github.io

Datasets:

metal_masterlist - A character vector of CyTOF metal name patterns supported by tidyFlowCore

On BioConductor:tidyFlowCore-1.7.0(bioc 3.24)tidyFlowCore-1.6.0(bioc 3.23)

singlecell flowcytometry infrastructure

4.51 score 2 stars 16 scripts 6 exports 42 dependencies

Last updated from:9f3a401979. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	185
linux-devel-x86_64	OK	266
source / vignettes	OK	293
linux-release-x86_64	OK	312
macos-release-arm64	OK	131
macos-oldrel-arm64	OK	184
windows-devel	OK	464
windows-release	OK	487
windows-oldrel	OK	456
wasm-release	OK	193

Exports::=.data as_flowFrame as_flowSet as_tof_tbl simulate_cytometry_data

Dependencies:BH Biobase BiocGenerics biocmake cli cpp11 cytolib dir.expiry dplyr farver filelock flowCore generics ggplot2 glue gtable isoband labeling lifecycle magrittr matrixStats pillar pkgconfig purrr R6 RColorBrewer Rcpp Rhdf5lib rlang RProtoBufLib S4Vectors S7 scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr

tidyFlowCore

Rendered fromtidyFlowCore.Rmdusingknitr::rmarkdown

Last update: 2024-05-03
Started: 2024-03-16

Help page	Topics
Order rows using column values	arrange.flowFrame
Order rows using column values	arrange.flowSet
Coerce an object into a 'flowFrame'	as_flowFrame as_flowFrame.tof_tbl
Coerce an object into a 'flowSet'	as_flowSet as_flowSet.tof_tbl
Coerce flowFrames or flowSets into tibbles.	as_tof_tbl
Convert an object into a tibble-flowCore abstraction (a `tof_tbl`)	as_tof_tbl.flowSet
Count the observations in each group.	count.flowFrame
Count the observations in each group.	count.flowSet
Keep rows that match a condition.	filter.flowFrame
Keep rows that match a condition.	filter.flowSet
Create a new ggplot.	ggplot.flowFrame
Create a new ggplot.	ggplot.flowSet
Group a flowFrame into a flowSet using one or more variables.	group_by.flowFrame
Make the AnnotatedDataFrame needed for the flowFrame class	make_flowcore_annotated_data_frame
A character vector of CyTOF metal name patterns supported by tidyFlowCore	metal_masterlist
Create, modify, and delete columns.	mutate.flowFrame
Create, modify, and delete columns.	mutate.flowSet
Nest a 'flowFrame' into a 'flowSet'	nest.flowFrame
Constructor for a tof_tibble.	new_tof_tibble
Extract a single column.	pull.flowFrame
Extract a single column.	pull.flowSet
Rename columns in a 'flowFrame'	rename_with.flowFrame
Rename columns in a 'flowSet'	rename_with.flowSet
Rename columns in a 'flowFrame'	rename.flowFrame
Rename columns in a 'flowSet'	rename.flowSet
Keep or drop columns using their names and types.	select.flowFrame
Keep or drop columns using their names and types.	select.flowSet
Simulate Cytometry Data for FlowSet and FlowFrame Analysis	simulate_cytometry_data
Subset rows at the head of a data structure.	slice_head.flowFrame
Subset rows at the head of a data structure.	slice_head.flowSet
Subset rows of a data structure in order.	slice_max.flowFrame
Subset rows of a data structure in order.	slice_max.flowSet
Subset rows of a data structure in order.	slice_min.flowFrame
Subset rows of a data structure in order.	slice_min.flowSet
Subset rows randomly	slice_sample.flowFrame
Subset rows randomly	slice_sample.flowSet
Subset rows at the tail of a data structure.	slice_tail.flowFrame
Subset rows at the tail of a data structure.	slice_tail.flowSet
Subset rows using their positions	slice.flowFrame
Subset rows using their positions	slice.flowSet
Summarize a flowFrame.	summarise.flowFrame
Summarize a flowSet.	summarise.flowSet
Summarize a flowFrame.	summarize.flowFrame
Summarize a flowSet.	summarize.flowSet
Use tidyFlowCore's opinionated heuristic for extracting a high-dimensional cytometry panel's channel-antigen pairs from a flowFrame (read from a .fcs file.)	tof_find_panel_info
Get panel information from a tof_tibble	tof_get_panel
Set panel information from a tof_tbl	tof_set_panel
Create, modify, and delete columns.	transmute.flowFrame
Create, modify, and delete columns.	transmute.flowSet
Ungroup a flowSet	ungroup.flowSet
Unnest a 'flowSet' into a single 'flowFrame'	unnest.flowSet

Package: tidyFlowCore 1.7.0

tidyFlowCore: tidyFlowCore: Bringing flowCore to the tidyverse

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