Package: CytoML 2.19.1

Mike Jiang

CytoML: A GatingML Interface for Cross Platform Cytometry Data Sharing

Uses platform-specific implemenations of the GatingML2.0 standard to exchange gated cytometry data with other software platforms.

Authors:Mike Jiang, Jake Wagner

CytoML_2.19.1.tar.gz
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CytoML.pdf |CytoML.html✨
CytoML/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/rglab/cytoml/issues

Uses libs:
  • zlib– Compression library
  • openblas– Optimized BLAS
  • libxml2– GNOME XML library
  • c++– GNU Standard C++ Library v3

On BioConductor:CytoML-2.19.1(bioc 3.21)CytoML-2.18.1(bioc 3.20)

immunooncologyflowcytometrydataimportdatarepresentationzlibopenblaslibxml2cpp

8.98 score 30 stars 132 scripts 954 downloads 4 mentions 35 exports 74 dependencies

Last updated 1 months agofrom:c84d4bd7a4. Checks:1 OK, 10 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 01 2025
R-4.5-win-x86_64WARNINGFeb 01 2025
R-4.5-mac-x86_64WARNINGFeb 01 2025
R-4.5-mac-aarch64WARNINGFeb 01 2025
R-4.5-linux-x86_64WARNINGFeb 01 2025
R-4.4-win-x86_64WARNINGFeb 01 2025
R-4.4-mac-x86_64WARNINGFeb 01 2025
R-4.4-mac-aarch64WARNINGFeb 01 2025
R-4.3-win-x86_64WARNINGFeb 01 2025
R-4.3-mac-x86_64WARNINGFeb 01 2025
R-4.3-mac-aarch64WARNINGFeb 01 2025

Exports:ce_get_channelsce_get_compensationsce_get_markersce_get_panelsce_get_samplesce_get_transformationscolnamescytobank_to_gatingsetcytobank2GatingSetcytobankExperimentdiva_get_sample_groupsdiva_get_samplesdiva_to_gatingsetextendfj_ws_get_keywordsfj_ws_get_sample_groupsfj_ws_get_samplesflowjo_to_gatingsetgatingset_to_cytobankgatingset_to_flowjoGatingSet2cytobankGatingSet2flowJogetKeywordsgetSampleGroupsgetSamplesgs_compare_cytobank_countsmarkernamesopen_cytobank_experimentopen_diva_xmlopen_flowjo_xmlopenDivaparseWorkspacepDatasampleNamesshow

Dependencies:abindBHBiobaseBiocGenericsclicolorspacecpp11crayoncytolibdata.tableDelayedArraydeldirdplyrfansifarverflowClustflowCoreflowVizflowWorkspacegenericsggcytoggplot2gluegraphgridExtragtablehexbinIDPmiscinterpIRangesisobandjpegjsonliteKernSmoothlabelinglatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmunsellncdfFlownlmeopenCytopillarpkgconfigplyrpngR6RBGLRColorBrewerRcppRcppEigenRgraphvizRhdf5librlangRProtoBufLibS4ArraysS4VectorsscalesSparseArraytibbletidyselectutf8vctrsviridisLitewithrXMLXVectoryaml

Import FlowJo workspace to R

Mike Jiang

Rendered fromflowjo_to_gatingset.Rmdusingknitr::rmarkdownon Feb 01 2025.

Last update: 2020-07-09
Started: 2020-07-03

How to export a GatingSet to GatingML

Mike Jiang

Rendered fromHowToExportGatingSet.Rmdusingknitr::rmarkdownon Feb 01 2025.

Last update: 2019-12-12
Started: 2016-05-25

How to import Cytobank into a GatingSet

Mike Jiang

Rendered fromcytobank2GatingSet.Rmdusingknitr::rmarkdownon Feb 01 2025.

Last update: 2021-02-27
Started: 2019-03-11

Readme and manuals

Help Manual

Help pageTopics
add customInfo nodes to each gate node and add BooleanAndGatesaddCustomInfo
Extract channels from cytobank_experimentce_get_channels
Obtain the spillover matrices for the samples in a Cytobank experimentce_get_compensations
Extract markers from cytobank_experimentce_get_markers
Obtain counts of the number of samples associated with each marker panel in a Cytobank experimentce_get_panels
Obtain a mapping between the samples and marker panels in a Cytobank experimentce_get_samples
Obtain the transformations associated with each channel in a Cytobank experimentce_get_transformations
compensate a GatingSet based on the compensation information stored in graphGML objectcompensate,GatingSet,graphGML-method
Reconstruct the population tree from the GateSetsconstructTree
Methods for interacting with cytobank_experiment objectscolnames,cytobank_experiment-method cytobank_experiment-methods markernames,cytobank_experiment-method pData,cytobank_experiment-method print.cytobank_experiment sampleNames,cytobank_experiment-method
A wrapper that parses the gatingML and FCS files (or 'cytobank_experiment' object) into GatingSetcytobank2GatingSet cytobank_to_gatingset cytobank_to_gatingset.cytobank_experiment cytobank_to_gatingset.default
Deprecated functions in package 'CytoML'.CytoML-deprecated
Get a table of samples from a FACSDiva workspacediva_get_samples diva_get_sample_groups
Parse a FACSDiva Workspacediva_to_gatingset parseWorkspace,diva_workspace-method
An R representation of a BD FACSDiva workspacediva_workspace-class show,diva_workspace-method
extend the gate to the minimum and maximum limit of both dimensions based on the bounding information.extend extend.ellipsoidGate extend.polygonGate extend.rectangleGate
Get Keywordsfj_ws_get_keywords getKeywords
Get a table of sample groups from a flowJo workspacefj_ws_get_sample_groups getSampleGroups
Get a list of samples from a flowJo workspacefj_ws_get_samples getSamples
An R representation of a flowJo workspace.flowjo_workspace-class show,flowjo_workspace-method
Convert a GatingSet to a Cytobank-compatible gatingMLGatingSet2cytobank gatingset_to_cytobank
Convert a GatingSet to flowJo workspaceGatingSet2flowJo gatingset_to_flowjo
get children nodesgetChildren,graphGML,character-method
Extract compensation from graphGML object.getCompensationMatrices.graphGML
get gate from the nodegetGate,graphGML,character-method
get nodes from graphGML objectgetNodes,graphGML-method
get parent nodesgetParent,graphGML,character-method
Extract transformations from graphGML object.getTransformations.graphGML
A graph object returned by 'read.gatingML.cytobank' function.graphGML-class
compare the counts to cytobank's exported csv so that the parsing result can be verified.gs_compare_cytobank_counts
Given the leaf node, try to find out if a collection of nodes can be matched to a path in a graph(tree) by the bottom-up searchingmatchPath
Construct a 'cytobank_experiment' object from ACS filecytobankExperiment open_cytobank_experiment
open Diva xml workspaceopenDiva open_diva_xml
Open/Close a flowJo workspaceopen_flowjo_xml
Parse the cytobank custom_info for each gateparse.gateInfo
Parse a flowJo Workspaceflowjo_to_gatingset parseWorkspace parseWorkspace,flowjo_workspace-method
plot the population tree stored in graphGML.plot,graphGML,missing-method
the parameter range from the flow data associated with GatingHierarchyrange.GatingHierarchy
Parser for gatingML exported by Cytobankread.gatingML.cytobank
show method for graphGMLshow,graphGML-method