MerfishData

DOI: 10.18129/B9.bioc.MerfishData  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see MerfishData.

Collection of public MERFISH datasets

Bioconductor version: 3.16

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 Mofitt [aut], Robert Gentleman [aut]

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

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

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

Details

biocViews	ExperimentData, ExperimentHub, ExpressionData, HighThroughputImagingData, Mus_musculus_Data, SingleCellData, SpatialData
Version	1.0.0
License	Artistic-2.0
Depends	R (>= 4.2.0), EBImage, SpatialExperiment
Imports	grDevices, AnnotationHub, BumpyMatrix, ExperimentHub, S4Vectors, SummarizedExperiment
LinkingTo
Suggests	grid, ggplot2, ggpubr, knitr, rmarkdown, testthat, BiocStyle, ExperimentHubData
SystemRequirements
Enhances
URL	https://github.com/ccb-hms/MerfishData
BugReports	https://github.com/ccb-hms/MerfishData/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	MerfishData_1.0.0.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/
Package Downloads Report	Download Stats