MerfishData

This is the development version of MerfishData; for the stable release version, see MerfishData.

Collection of public MERFISH datasets

Bioconductor version: Development (3.21)

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.

Author: Ludwig Geistlinger [aut, cre] (ORCID: ), Tyrone Lee [ctb], Helena Crowell [ctb] (ORCID: ), Daniela Corbetta [ctb], Jeffrey Moffitt [aut], Robert Gentleman [aut]

Maintainer: Ludwig Geistlinger <ludwig_geistlinger at hms.harvard.edu>

Citation (from within R, enter citation("MerfishData")):

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("MerfishData")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MerfishData")

Mouse colon ibd	HTML	R Script
Mouse hypothalamus	HTML	R Script
Mouse ileum	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData, ExperimentHub, ExpressionData, HighThroughputImagingData, Mus_musculus_Data, SingleCellData, SpatialData
Version	1.9.0
License	Artistic-2.0
Depends	R (>= 4.2.0), EBImage, SpatialExperiment
Imports	grDevices, AnnotationHub, BumpyMatrix, ExperimentHub, S4Vectors, SingleCellExperiment, SummarizedExperiment, HDF5Array
System Requirements
URL	https://github.com/ccb-hms/MerfishData
Bug Reports	https://github.com/ccb-hms/MerfishData/issues

Suggests	grid, ggplot2, ggpubr, knitr, rmarkdown, scater, scattermore, terra, testthat, BiocStyle, DropletUtils
Linking To
Enhances
Depends On Me
Imports Me
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Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	MerfishData_1.9.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/MerfishData
Source Repository (Developer Access)	git clone [email protected]:packages/MerfishData
Package Short Url	https://bioconductor.org/packages/MerfishData/
Package Downloads Report	Download Stats