.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 |