MerfishData
Collection of public MERFISH datasets
Bioconductor version: Release (3.20)
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] , Daniela Corbetta [ctb], Jeffrey Moffitt [aut], Robert Gentleman [aut]
Maintainer: Ludwig Geistlinger <ludwig_geistlinger at hms.harvard.edu>
citation("MerfishData")):
Installation
To install this package, start R (version "4.4") 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")| Mouse colon ibd | HTML | R Script |
| Mouse hypothalamus | HTML | R Script |
| Mouse ileum | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, ExperimentHub, ExpressionData, HighThroughputImagingData, Mus_musculus_Data, SingleCellData, SpatialData |
| Version | 1.7.1 |
| 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 |
See More
| Suggests | grid, ggplot2, ggpubr, knitr, rmarkdown, scater, scattermore, terra, testthat, BiocStyle, DropletUtils |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MerfishData_1.7.1.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 git@git.bioconductor.org:packages/MerfishData |
| Package Short Url | https://bioconductor.org/packages/MerfishData/ |
| Package Downloads Report | Download Stats |