Package: IFC 0.2.1.707

IFC: Tools for Imaging Flow Cytometry

Contains several tools to treat imaging flow cytometry data from 'ImageStream®' and 'FlowSight®' cytometers ('Amnis®' 'Cytek®'). Provides an easy and simple way to read and write .fcs, .rif, .cif and .daf files. Information such as masks, features, regions and populations set within these files can be retrieved for each single cell. In addition, raw data such as images stored can also be accessed. Users, may hopefully increase their productivity thanks to dedicated functions to extract, visualize, manipulate and export 'IFC' data. Toy data example can be installed through the 'IFCdata' package of approximately 32 MB, which is available in a 'drat' repository <https://gitdemont.github.io/IFCdata/>. See file 'COPYRIGHTS' and file 'AUTHORS' for a list of copyright holders and authors.

Authors:Yohann Demont [aut, cre], Gautier Stoll [ctb], Guido Kroemer [ldr], Jean-Pierre Marolleau [ldr], Loïc Garçon [ldr]

IFC_0.2.1.707.tar.gz
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IFC.pdf |IFC.html✨
IFC/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/gitdemont/ifc/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

cytometrycytometry-dataflowflow-cytometryflow-cytometry-analysisflow-cytometry-dataflow-cytometry-filesifcimageimaging-flow-cytometryimaging-flow-cytometry-datamicroscopy

5.32 score 4 stars 11 scripts 329 downloads 4 mentions 57 exports 50 dependencies

Last updated 1 days agofrom:b35cd59342. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 22 2024
R-4.5-win-x86_64NOTENov 22 2024
R-4.5-linux-x86_64NOTENov 22 2024
R-4.4-win-x86_64NOTENov 22 2024
R-4.4-mac-x86_64NOTENov 22 2024
R-4.4-mac-aarch64NOTENov 22 2024
R-4.3-win-x86_64NOTENov 22 2024
R-4.3-mac-x86_64NOTENov 22 2024
R-4.3-mac-aarch64NOTENov 22 2024

Exports:autoplotBatchReportbuildBatchbuildFeaturebuildGraphbuildPopulationbuildRegionchecksumIFCdata_add_featuresdata_add_graphsdata_add_popsdata_add_regionsdata_rm_featuresdata_rm_graphsdata_rm_popsdata_rm_regionsdata_to_DAFDisplayGalleryExportToBATCHExportToDAFExportToFCSExportToGalleryExportToNumpyExportToReportExportToXIFExtractFromDAFExtractFromFCSExtractFromXIFExtractImages_toBase64ExtractImages_toFileExtractImages_toMatrixExtractImages_toMultiExtractMasks_toBase64ExtractMasks_toFileExtractMasks_toMatrixExtractMasks_toMultigetAbortedgetFullTaggetIFDgetInfogetOffsetsinv_smoothLinLogobjectDisplayobjectExtractobjectParampaletteIFCplotGraphpopsComputepopsCopypopsGetObjectsIdspopsNetworkpopsRenamereadFCSreadIFCsmoothLinLogsubsetOffsetswriteIFC

Dependencies:base64encbslibcachemclicrosstalkdeldirdigestDTevaluatefastmapfontawesomefsgluegridExtragridGraphicsgtablehighrhtmltoolshtmlwidgetshttpuvinterpjpegjquerylibjsonliteKernSmoothknitrlaterlatticelatticeExtralazyevallifecyclemagrittrMASSmemoisemimepngpromisesR6rappdirsRColorBrewerRcppRcppEigenrlangrmarkdownsasstinytexvisNetworkxfunxml2yaml

Readme and manuals

Help Manual

Help pageTopics
Tools for Imaging Flow CytometryIFC-package IFC
Automatic Parameters Detection for IFC Graphsautoplot
Batch Generation of Graphical and Statistic ReportBatchReport
Batch BuilderbuildBatch
IFC Feature CoercionbuildFeature
IFC Graph CoercionbuildGraph
IFC Population CoercionbuildPopulation
IFC Region CoercionbuildRegion
IFC Files ChecksumchecksumIFC
IFD Tag Writercpp_writeIFD
Add Feature to IFC_data Objectdata_add_features
Add Graphs to IFC_data Objectdata_add_graphs
Add Population to IFC_data Objectdata_add_pops
Add Region to IFC_data Objectdata_add_regions
Remove Features from an IFC_data Objectdata_rm_features
Remove Graph from an IFC_data Objectdata_rm_graphs
Remove Population from an IFC_data Objectdata_rm_pops
Remove Region from an IFC_data Objectdata_rm_regions
DAF File Writerdata_to_DAF
Gallery DisplayDisplayGallery
Batch File WriterExportToBATCH
DAF File WriterExportToDAF
FCS File WriterExportToFCS
Gallery ExportExportToGallery
Numpy ExportExportToNumpy
Graphical and Statistic Report GenerationExportToReport
RIF/CIF File WriterExportToXIF
DAF File ReaderExtractFromDAF
FCS File ReaderExtractFromFCS
RIF/CIF File ReaderExtractFromXIF
Shortcut for Batch Images Extraction to Base64ExtractImages_toBase64
Shortcut for Batch Images Extraction to FilesExtractImages_toFile
Shortcut for Batch Images Extraction to Matrices/ArraysExtractImages_toMatrix
Shortcut for Batch Images Extraction to Multichannel TiffExtractImages_toMulti
Shortcut for Batch Masks Extraction to Base64ExtractMasks_toBase64
Shortcut for Batch Masks Extraction to FilesExtractMasks_toFile
Shortcut for Batch Masks Extraction to Matrices/ArraysExtractMasks_toMatrix
Shortcut for Batch Masks Extraction to Multichannel TiffExtractMasks_toMulti
Alternative Names Generatorgen_altnames
Aborted Batch Files RetrievalgetAborted
Image Field Directory Full Tag RetrievalgetFullTag
RIF/CIF Image Field Directories ExtractiongetIFD
IFC File Information ExtractiongetInfo
RIF/CIF File Image Field Directories Offsets ExtractiongetOffsets
Inverse Smooth LinLog Transformationinv_smoothLinLog
Object CleanserobjectCleanse
Object DisplayobjectDisplay
Object ExtractionobjectExtract
Object Extraction Parameters DefinitionobjectParam
R/IDEAS Color Palette MappingpaletteIFC
Plot and Stats Computation for IFC GraphplotGraph
IFC_pops ComputationpopsCompute
Copy Populations from One File to Another FilepopsCopy
IFC_pops Object NumberspopsGetObjectsIds
IFC_pops Network DisplaypopsNetwork
Populations RenamingpopsRename
FCS File ParserreadFCS
IFC Files Generic ReaderreadIFC
Smooth LinLog TransformationsmoothLinLog
IFC_offset SubsettingsubsetOffsets
IFC Files Generic WriterwriteIFC