Function reference • MoleculeExperiment

All functions

MoleculeExperiment(): MoleculeExperiment class: An S4 class container to store imaging-based spatial transcriptomics data.

molecules(<MoleculeExperiment>) boundaries(<MoleculeExperiment>) features(<MoleculeExperiment>) segmentIDs(<MoleculeExperiment>) `molecules<-`(<MoleculeExperiment>) `boundaries<-`(<MoleculeExperiment>): 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

.generateBPParam(): Utility function to generate BPPARAM object.

ggplot_me() geom_point_me() geom_polygon_me(): 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

small_me: A subsetted Xenium dataset include for demostration purposes.

show(<MoleculeExperiment>) showMolecules(<MoleculeExperiment>) showBoundaries(<MoleculeExperiment>) extent(<MoleculeExperiment>) nFeatures(<MoleculeExperiment>) nTranscripts(<MoleculeExperiment>): Summarization methods to get insights into a MoleculeExperiment object