Package: CytoML 2.25.0

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_2.25.0.tar.gz
CytoML_2.25.0.zip(r-4.7)CytoML_2.25.0.zip(r-4.6)CytoML_2.25.0.zip(r-4.5)
CytoML_2.25.0.tgz(r-4.6-x86_64)CytoML_2.25.0.tgz(r-4.6-arm64)CytoML_2.25.0.tgz(r-4.5-x86_64)CytoML_2.25.0.tgz(r-4.5-arm64)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CytoML/json (API)

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

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

Uses libs:
  • curl– Easy-to-use client-side URL transfer library
  • openssl– Secure Sockets Layer toolkit
  • openblas– Optimized BLAS
  • libxml2– GNOME XML library
  • c++– GNU Standard C++ Library v3

On BioConductor:CytoML-2.25.0(bioc 3.24)CytoML-2.24.0(bioc 3.23)

immunooncologyflowcytometrydataimportdatarepresentationcurlopensslopenblaslibxml2cpp

9.45 score 35 stars 338 scripts 4 mentions 35 exports 72 dependencies

Last updated from:395d974a61. Checks:1 ERROR, 11 WARNING, 1 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR222
linux-devel-arm64WARNING287
linux-devel-x86_64WARNING312
source / vignettesOK389
linux-release-arm64WARNING302
linux-release-x86_64WARNING296
macos-release-arm64WARNING212
macos-release-x86_64WARNING379
macos-oldrel-arm64WARNING178
macos-oldrel-x86_64WARNING442
windows-develWARNING390
windows-releaseWARNING400
windows-oldrelWARNING427
wasm-releaseFAIL194

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:abindBHBiobaseBiocGenericsbiocmakeclicpp11cytolibdata.tableDelayedArraydeldirdir.expirydplyrfarverfilelockflowClustflowCoreflowVizflowWorkspacegenericsggcytoggplot2gluegraphgridExtragtablehexbinIDPmiscinterpIRangesisobandjpegjsonliteKernSmoothlabelinglatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsncdfFlowopenCytopillarpkgconfigplyrpngR6RBGLRColorBrewerRcppRcppEigenRgraphvizRhdf5librlangRProtoBufLibS4ArraysS4VectorsS7scalesSparseArraytibbletidyselectutf8vctrsviridisLitewithrXMLXVectoryaml

How to export a GatingSet to GatingML
Automated gating | Load raw FCS files into GatingSet | Compensate and transform | Load the gating template and run auto gating | Export to Cytobank | Export to FlowJo
Rendered fromHowToExportGatingSet.Rmdusingknitr::rmarkdown

Last update: 2025-03-03
Started: 2016-05-25

How to import Cytobank into a GatingSet
Rendered fromcytobank2GatingSet.Rmdusingknitr::rmarkdown

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

Import FlowJo workspace to R
Basics | open the workspace | Extract groups from xml | Extract Samples from xml | Extract keywords from xml | Parse with default settings | select group | FCS path | string | data.frame | Advanced | Parsing xml without loading FCS | Additional keys to tag samples | additional.keys | additional.sampleID | Annotate sample with keywords | keywords | keywords.source | keyword.ignore.case | Import a subset | Parallel parsing | Skip leaf boolean gates | Skip faulty gates | Import the empty gating tree | Customized fcs file extension
Rendered fromflowjo_to_gatingset.Rmdusingknitr::rmarkdown

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

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