Package: scpImaging 0.9.9.2

Edward Emmott

scpImaging: Functions for handling cellenONE-based imaging data for single-cell experiments

This package includes functions for curating, manipulating, and visualising cellenONE-based imaging data for single-cell experiments. It is designed to work with microscopy images and associated metadata produced on the cellenONE platform, which is a high-throughput imaging and handling system for single-cell analysis. It contains functions to process the initial images for downstream analysis in cellPose and cellProfiler, as well as for importing and processing the data output from these pipelines. It also contains a module for interactive visualisation of cellenONE-based images using the iSEE package for interactive single-cell experiment exploration.

Authors:Edward Emmott [aut, cre]

scpImaging_0.9.9.2.tar.gz
scpImaging_0.9.9.2.zip(r-4.7)scpImaging_0.9.9.2.zip(r-4.6)scpImaging_0.9.9.2.zip(r-4.5)
scpImaging_0.9.9.2.tgz(r-4.6-any)scpImaging_0.9.9.2.tgz(r-4.5-any)
scpImaging_0.9.9.2.tar.gz(r-4.7-any)scpImaging_0.9.9.2.tar.gz(r-4.6-any)
scpImaging_0.9.9.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
scpImaging/json (API)

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

Bug tracker:https://github.com/emmottlab/scpimaging/issues

On CRAN:

Conda:

2.88 score 3 stars 1 scripts 23 exports 131 dependencies

Last updated from:ca948ba151. Checks:7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING340
source / vignettesOK214
linux-release-x86_64WARNING319
macos-release-arm64WARNING214
macos-oldrel-arm64WARNING179
windows-develWARNING291
windows-releaseWARNING336
windows-oldrelWARNING326
wasm-releaseOK164

Exports:.defineDataInterface.defineOutput.definePanelTour.exportOutput.fullName.generateOutput.hideInterface.panelColor.refineParameters.renderOutput.singleSelectionSlotsaddCellProfilerAttributesaddCellProfilerAttributesSCECellenONEPlotcleanFilenamescountCellscropImagesgenerateImageColumnsgenerateImageColumnsSCEinitializenpyMasksToPngoverlayMaskoverlayMaskOnParent

Dependencies:abindAnnotationFilteraskpassbase64encBiobaseBiocBaseUtilsBiocGenericsbslibcachemcirclizecliclueclustercodetoolscolorspacecolourpickercommonmarkComplexHeatmapcpp11crayoncrosstalkcurldata.tableDelayedArraydigestdoParalleldplyrDTevaluatefarverfastmapfontawesomeforeachfsgenericsGenomicRangesGetoptLongggplot2ggrepelGlobalOptionsgluegtableherehighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesiSEEisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelistviewermagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUIMsCoreUtilsMultiAssayExperimentnlmeopensslotelpatchworkpillarpkgconfigplotlyplyrpngpromisesProtGenericspurrrQFeaturesR6rappdirsRColorBrewerRcppRcppTOMLreshape2reticulaterintrojsrjsonrlangrmarkdownrprojrootS4ArraysS4VectorsS7sassscalesSeqinfoshapeshinyshinyAceshinydashboardshinyjsshinyWidgetsSingleCellExperimentsourcetoolsSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviporviridisLitewithrxfunxtableXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
'addCellProfilerAttributes()': Add Attributes from a Second Data Frame Based on KeysaddCellProfilerAttributes
'addCellProfilerAttributesSCE()': Add CellProfiler Attributes to colData of Bioconductor ObjectsaddCellProfilerAttributesSCE
Create an Instance of a CellenONEPlot PanelCellenONEPlot
The CellenONEPlot Class.defineDataInterface,CellenONEPlot-method .defineOutput,CellenONEPlot-method .definePanelTour,CellenONEPlot-method .exportOutput,CellenONEPlot-method .fullName,CellenONEPlot-method .generateOutput,CellenONEPlot-method .hideInterface,CellenONEPlot-method .panelColor,CellenONEPlot-method .refineParameters,CellenONEPlot-method .renderOutput,CellenONEPlot-method .singleSelectionSlots,CellenONEPlot-method CellenONEPlot-class initialize,CellenONEPlot-method
'cleanFilenames()': Clean Hyperlink Formatting from DataFrame ColumnscleanFilenames
'countCells()':Count Unique Masks in PNG Segmentation MaskscountCells
'cropImages()': Generate Cropped Images from Image Paths and CoordinatescropImages
generateImageColumns(): Generate Derived Image File ColumnsgenerateImageColumns
'generateImageColumnsSCE():' Apply generateImageColumns to Bioconductor Object colDatagenerateImageColumnsSCE generateImageColumnsSCE,QFeatures-method generateImageColumnsSCE,SummarizedExperiment-method
'npyMasksToPng()' converts Cellpose.npy Masks to PNG ImagesnpyMasksToPng
'overlayMask()': Overlay Segmentation Mask on Image (Single File or Directory)overlayMask
'overlayMaskOnParent()': Overlay Segmentation Masks onto Parent Images at Specific CoordinatesoverlayMaskOnParent