Prioritising a molecule-level storage of Spatial Transcriptomics Data


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Documentation for package ‘MoleculeExperiment’ version 1.8.0

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.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