Prioritising a molecule-level storage of Spatial Transcriptomics Data

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Documentation for package ‘MoleculeExperiment’ version 1.9.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

.generateBPParam	Utility function to generate BPPARAM object.
accessors	Accessor functions to work with MoleculeExperiment objects
boundaries	Accessor functions to work with MoleculeExperiment objects
boundaries-method	Accessor functions to work with MoleculeExperiment objects
boundaries<-	Accessor functions to work with MoleculeExperiment objects
boundaries<--method	Accessor functions to work with MoleculeExperiment objects
bufferBoundaries	Create a new boundaries assay with buffers
countMolecules	Count molecules per region of interest (e.g., cell)
dataframeToMEList	Convert a transcript (molecule) or boundary dataframe to the ME list format
extent	Summarization methods to get insights into a MoleculeExperiment object
extent-method	Summarization methods to get insights into a MoleculeExperiment object
features	Accessor functions to work with MoleculeExperiment objects
features-method	Accessor functions to work with MoleculeExperiment objects
geom_point_me	Plotting functions for SpatialUtils
geom_polygon_me	Plotting functions for SpatialUtils
geom_raster_img	Plotting functions for SpatialUtils
ggplot_me	Plotting functions for SpatialUtils
MoleculeExperiment	MoleculeExperiment class: An S4 class container to store imaging-based spatial transcriptomics data.
MoleculeExperiment-class	MoleculeExperiment class: An S4 class container to store imaging-based spatial transcriptomics data.
molecules	Accessor functions to work with MoleculeExperiment objects
molecules-method	Accessor functions to work with MoleculeExperiment objects
molecules<-	Accessor functions to work with MoleculeExperiment objects
molecules<--method	Accessor functions to work with MoleculeExperiment objects
nFeatures	Summarization methods to get insights into a MoleculeExperiment object
nFeatures-method	Summarization methods to get insights into a MoleculeExperiment object
nTranscripts	Summarization methods to get insights into a MoleculeExperiment object
nTranscripts-method	Summarization methods to get insights into a MoleculeExperiment object
plotting-functions	Plotting functions for SpatialUtils
readBoundaries	Read in csv boundary information and convert to ME list format.
readCosmx	Read in Cosmx data (Nanostring) as an ME object.
readMerscope	Read in Merscope data to an ME object
readMolecules	Read in detected transcripts file/s into a MoleculeExperiment object
readSegMask	Read a segmentation mask
readXenium	Read in Xenium data into a MoleculeExperiment object
segmentIDs	Accessor functions to work with MoleculeExperiment objects
segmentIDs-method	Accessor functions to work with MoleculeExperiment objects
show-method	Summarization methods to get insights into a MoleculeExperiment object
showBoundaries	Summarization methods to get insights into a MoleculeExperiment object
showBoundaries-method	Summarization methods to get insights into a MoleculeExperiment object
showMolecules	Summarization methods to get insights into a MoleculeExperiment object
showMolecules-method	Summarization methods to get insights into a MoleculeExperiment object
small_me	A subsetted Xenium dataset include for demostration purposes.
subset_by_extent	Subset functions for MoleculeExperiment objects
summarization	Summarization methods to get insights into a MoleculeExperiment object