Package: tidyFlowCore 1.1.0

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_1.1.0.tar.gz
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tidyFlowCore.pdf |tidyFlowCore.html✨
tidyFlowCore/json (API)
NEWS

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

Peer review:

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

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

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

On BioConductor:tidyFlowCore-1.1.0(bioc 3.21)tidyFlowCore-1.0.0(bioc 3.20)

singlecellflowcytometryinfrastructure

4.40 score 1 stars 7 scripts 76 downloads 6 exports 46 dependencies

Last updated 2 months agofrom:a9a0990aee. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 01 2024
R-4.5-winOKDec 01 2024
R-4.5-linuxOKDec 01 2024
R-4.4-winOKDec 01 2024
R-4.4-macOKDec 01 2024
R-4.3-winOKDec 01 2024
R-4.3-macOKDec 01 2024

Exports::=.dataas_flowFrameas_flowSetas_tof_tblsimulate_cytometry_data

Dependencies:BHBiobaseBiocGenericsclicolorspacecpp11cytolibdplyrfansifarverflowCoregenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmatrixStatsmgcvmunsellnlmepillarpkgconfigpurrrR6RColorBrewerRcppRhdf5librlangRProtoBufLibS4Vectorsscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

tidyFlowCore

Timothy Keyes

Rendered fromtidyFlowCore.Rmdusingknitr::rmarkdownon Dec 01 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Order rows using column valuesarrange.flowFrame
Order rows using column valuesarrange.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 classmake_flowcore_annotated_data_frame
A character vector of CyTOF metal name patterns supported by tidyFlowCoremetal_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 Analysissimulate_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 randomlyslice_sample.flowFrame
Subset rows randomlyslice_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 positionsslice.flowFrame
Subset rows using their positionsslice.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_tibbletof_get_panel
Set panel information from a tof_tbltof_set_panel
Create, modify, and delete columns.transmute.flowFrame
Create, modify, and delete columns.transmute.flowSet
Ungroup a flowSetungroup.flowSet
Unnest a 'flowSet' into a single 'flowFrame'unnest.flowSet