Bioc2026 Registration Open!

MerfishData

Collection of public MERFISH datasets

Bioconductor version: 3.23 · Package version: 1.14.1

MerfishData is an ExperimentHub package that serves publicly available datasets obtained with Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH). MERFISH is a massively multiplexed single-molecule imaging technology capable of simultaneously measuring the copy number and spatial distribution of hundreds to tens of thousands of RNA species in individual cells. The scope of the package is to provide MERFISH data for benchmarking and analysis.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MerfishData")

Details

MaintainerLudwig Geistlinger <ludwig_geistlinger@hms.harvard.edu>
AuthorLudwig Geistlinger [aut, cre] (ORCID: <https://orcid.org/0000-0002-2495-5464>), Tyrone Lee [ctb], Helena Crowell [ctb] (ORCID: <https://orcid.org/0000-0002-4801-1767>), Daniela Corbetta [ctb], Jeffrey Moffitt [aut], Robert Gentleman [aut]
LicenseArtistic-2.0
URLhttps://github.com/ccb-hms/MerfishData
Bug Reportshttps://github.com/ccb-hms/MerfishData/issues
Downloads rank119
Source branchRELEASE_3_23
biocViewsExperimentData, ExperimentHub, ExpressionData, HighThroughputImagingData, Mus_musculus_Data, SingleCellData, SpatialData

Download

Dependencies

Depends: R (>= 4.2.0), EBImage, SpatialExperiment

Imports: grDevices, AnnotationHub, BumpyMatrix, ExperimentHub, S4Vectors, SingleCellExperiment, SummarizedExperiment, HDF5Array

Suggests: grid, ggplot2, ggpubr, knitr, rmarkdown, scater, scattermore, terra, testthat, BiocStyle, DropletUtils

Reverse dependencies

Suggests Me (1): scConform