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MerfishData

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

Collection of public MERFISH datasets


Bioconductor version: Development (3.19)

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] , Tyrone Lee [ctb], Helena Crowell [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 "4.4") 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 hypothalamus HTML R Script
Mouse ileum HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ExperimentData, ExperimentHub, ExpressionData, HighThroughputImagingData, Mus_musculus_Data, SingleCellData, SpatialData
Version 1.5.0
License Artistic-2.0
Depends R (>= 4.2.0), EBImage, SpatialExperiment
Imports grDevices, AnnotationHub, BumpyMatrix, ExperimentHub, S4Vectors, SingleCellExperiment, SummarizedExperiment
System Requirements
URL https://github.com/ccb-hms/MerfishData
Bug Reports https://github.com/ccb-hms/MerfishData/issues
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Suggests grid, ggplot2, ggpubr, knitr, rmarkdown, testthat, BiocStyle, DropletUtils
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Package Archives

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

Source Package MerfishData_1.5.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/MerfishData
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MerfishData
Package Short Url https://bioconductor.org/packages/MerfishData/
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