MoleculeExperiment | Why the MoleculeExperiment class? | Installation | Minimal example | The ME object in detail | Constructing an ME object | Use case 1: from dataframes to ME object | Use case 2: from machine's output directory to ME object | ME object structure | molecules slot | boundaries slot | Methods | Getters | Setters | Subsetting | From MoleculeExperiment to SpatialExperiment | Case Study: MoleculeExperiment and napari | SessionInfo
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:
MoleculeExperiment_1.13.0.tar.gz
MoleculeExperiment_1.13.0.zip(r-4.7)MoleculeExperiment_1.13.0.zip(r-4.6)MoleculeExperiment_1.13.0.zip(r-4.5)
MoleculeExperiment_1.13.0.tgz(r-4.6-any)MoleculeExperiment_1.13.0.tgz(r-4.5-any)
MoleculeExperiment_1.13.0.tar.gz(r-4.7-any)MoleculeExperiment_1.13.0.tar.gz(r-4.6-any)
MoleculeExperiment_1.13.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MoleculeExperiment/json (API)
| # 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
Last updated from:1b1963e54c. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 213 | ||
| linux-devel-x86_64 | NOTE | 457 | ||
| source / vignettes | OK | 325 | ||
| linux-release-x86_64 | NOTE | 458 | ||
| macos-release-arm64 | NOTE | 273 | ||
| macos-oldrel-arm64 | NOTE | 269 | ||
| windows-devel | NOTE | 390 | ||
| windows-release | NOTE | 390 | ||
| windows-oldrel | NOTE | 360 | ||
| wasm-release | OK | 217 |
Exports:boundariesboundaries<-bufferBoundariescountMoleculesdataframeToMEListextentfeaturesgeom_point_megeom_polygon_megeom_raster_imgggplot_meMoleculeExperimentmoleculesmolecules<-nFeaturesnTranscriptsreadBoundariesreadCosmxreadMerscopereadMoleculesreadSegMaskreadXeniumsegmentIDsshowBoundariesshowMoleculessubset_by_extent
Dependencies:abindaskpassbase64encBHBiobaseBiocFileCacheBiocGenericsbiocmakeBiocParallelbitbit64bitopsblobbslibcachemclicodetoolscpp11curldata.tableDBIdbplyrDelayedArraydigestdir.expirydplyrEBImageevaluatefarverfastmapfftwtoolsfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttr2IRangesisobandjpegjquerylibjsonliteknitrlabelinglambda.rlatticelifecyclelocfitmagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngpurrrR6rappdirsRColorBrewerRcppRCurlrhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownRSQLiteS4ArraysS4VectorsS7sassscalesSeqinfoSingleCellExperimentsnowSparseArraySpatialExperimentstringistringrSummarizedExperimentsysterratibbletidyrtidyselecttifftinytexutf8vctrsviridisLitewithrxfunXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Utility function to generate BPPARAM object. | .generateBPParam |
| Accessor functions to work with MoleculeExperiment objects | accessors 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 buffers | bufferBoundaries |
| Count molecules per region of interest (e.g., cell) | countMolecules |
| Convert a transcript (molecule) or boundary dataframe to the ME list format | dataframeToMEList |
| MoleculeExperiment class: An S4 class container to store imaging-based spatial transcriptomics data. | MoleculeExperiment MoleculeExperiment-class |
| Plotting functions for SpatialUtils | geom_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 object | readMerscope |
| Read in detected transcripts file/s into a MoleculeExperiment object | readMolecules |
| Read a segmentation mask | readSegMask |
| Read in Xenium data into a MoleculeExperiment object | readXenium |
| A subsetted Xenium dataset include for demostration purposes. | small_me |
| Subset functions for MoleculeExperiment objects | subset_by_extent |
| Summarization methods to get insights into a MoleculeExperiment object | extent extent,MoleculeExperiment-method nFeatures nFeatures,MoleculeExperiment-method nTranscripts nTranscripts,MoleculeExperiment-method show,MoleculeExperiment-method showBoundaries showBoundaries,MoleculeExperiment-method showMolecules showMolecules,MoleculeExperiment-method summarization |
