Prioritising a molecule-level storage of Spatial Transcriptomics Data

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Documentation for package ‘MoleculeExperiment’ version 1.0.1

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

Help Pages

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
countMolecules	Count molecules per region of interest (e.g., cell)
dataframeToMEList	Convert a transcripts or boundaries file to the ME list format
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
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
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
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
summarization	Summarization methods to get insights into a MoleculeExperiment object