# Prioritising a molecule-level storage of Spatial Transcriptomics Data

## Documentation for package ‘MoleculeExperiment’ version 1.11.0

- 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