Package: MoleculeExperiment 1.13.0

Shila Ghazanfar

MoleculeExperiment: Prioritising a molecule-level storage of Spatial Transcriptomics Data

MoleculeExperiment contains functions to create and work with objects from the new MoleculeExperiment class. We introduce this class for analysing molecule-based spatial transcriptomics data (e.g., Xenium by 10X, Cosmx SMI by Nanostring, and Merscope by Vizgen). This allows researchers to analyse spatial transcriptomics data at the molecule level, and to have standardised data formats accross vendors.

Authors:Bárbara Zita Peters Couto [aut], Nicholas Robertson [aut], Ellis Patrick [aut], Shila Ghazanfar [aut, cre]

MoleculeExperiment_1.13.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
MoleculeExperiment/json (API)
NEWS

# Install 'MoleculeExperiment' in R:
install.packages('MoleculeExperiment', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sydneybiox/moleculeexperiment/issues

Datasets:
  • small_me - A subsetted Xenium dataset include for demostration purposes.

On BioConductor:MoleculeExperiment-1.13.0(bioc 3.24)MoleculeExperiment-1.12.0(bioc 3.23)

dataimportdatarepresentationinfrastructuresoftwarespatialtranscriptomics

6.32 score 12 stars 44 scripts 305 downloads 26 exports 108 dependencies

Last updated from:1b1963e54c. Checks:8 NOTE, 2 OK. Indexed: yes.

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Exports:boundariesboundaries<-bufferBoundariescountMoleculesdataframeToMEListextentfeaturesgeom_point_megeom_polygon_megeom_raster_imgggplot_meMoleculeExperimentmoleculesmolecules<-nFeaturesnTranscriptsreadBoundariesreadCosmxreadMerscopereadMoleculesreadSegMaskreadXeniumsegmentIDsshowBoundariesshowMoleculessubset_by_extent

Dependencies:abindaskpassbase64encBHBiobaseBiocFileCacheBiocGenericsbiocmakeBiocParallelbitbit64bitopsblobbslibcachemclicodetoolscpp11curldata.tableDBIdbplyrDelayedArraydigestdir.expirydplyrEBImageevaluatefarverfastmapfftwtoolsfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttr2IRangesisobandjpegjquerylibjsonliteknitrlabelinglambda.rlatticelifecyclelocfitmagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngpurrrR6rappdirsRColorBrewerRcppRCurlrhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownRSQLiteS4ArraysS4VectorsS7sassscalesSeqinfoSingleCellExperimentsnowSparseArraySpatialExperimentstringistringrSummarizedExperimentsysterratibbletidyrtidyselecttifftinytexutf8vctrsviridisLitewithrxfunXVectoryaml

An introduction to the MoleculeExperiment Class

Bárbara Zita Peters Couto, Nick Robertson, Mu-Wei Chung, Ellis Patrick, Shila Ghazanfar

Rendered fromMoleculeExperiment.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2024-04-04
Started: 2023-03-29

Readme and manuals

Help Manual

Help pageTopics
Utility function to generate BPPARAM object..generateBPParam
Accessor functions to work with MoleculeExperiment objectsaccessors boundaries boundaries,MoleculeExperiment-method boundaries<- boundaries<-,MoleculeExperiment-method features features,MoleculeExperiment-method molecules molecules,MoleculeExperiment-method molecules<- molecules<-,MoleculeExperiment-method segmentIDs segmentIDs,MoleculeExperiment-method
Create a new boundaries assay with buffersbufferBoundaries
Count molecules per region of interest (e.g., cell)countMolecules
Convert a transcript (molecule) or boundary dataframe to the ME list formatdataframeToMEList
MoleculeExperiment class: An S4 class container to store imaging-based spatial transcriptomics data.MoleculeExperiment MoleculeExperiment-class
Plotting functions for SpatialUtilsgeom_point_me geom_polygon_me geom_raster_img ggplot_me plotting-functions
Read in csv boundary information and convert to ME list format.readBoundaries
Read in Cosmx data (Nanostring) as an ME object.readCosmx
Read in Merscope data to an ME objectreadMerscope
Read in detected transcripts file/s into a MoleculeExperiment objectreadMolecules
Read a segmentation maskreadSegMask
Read in Xenium data into a MoleculeExperiment objectreadXenium
A subsetted Xenium dataset include for demostration purposes.small_me
Subset functions for MoleculeExperiment objectssubset_by_extent
Summarization methods to get insights into a MoleculeExperiment objectextent extent,MoleculeExperiment-method nFeatures nFeatures,MoleculeExperiment-method nTranscripts nTranscripts,MoleculeExperiment-method show,MoleculeExperiment-method showBoundaries showBoundaries,MoleculeExperiment-method showMolecules showMolecules,MoleculeExperiment-method summarization