Package: MerfishData 1.14.1

Ludwig Geistlinger

MerfishData: Collection of public MERFISH datasets

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.

Authors:Ludwig Geistlinger [aut, cre], Tyrone Lee [ctb], Helena Crowell [ctb], Daniela Corbetta [ctb], Jeffrey Moffitt [aut], Robert Gentleman [aut]

MerfishData_1.14.1.tar.gz
MerfishData_1.14.1.tar.gz(r-4.7-any)MerfishData_1.14.1.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MerfishData/json (API)

# Install 'MerfishData' in R:

install.packages('MerfishData', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ccb-hms/merfishdata/issues

On BioConductor:MerfishData-1.15.1(data/experiment 3.24)MerfishData-1.14.1(data/experiment 3.23)

experimenthub expressiondata highthroughputimagingdata mus_musculus_data singlecelldata spatialdata datapkg

3.73 score 1 stars 18 scripts 7 exports 102 dependencies

Last updated from:8300466039 (on RELEASE_3_23). Checks:1 NOTE, 2 WARNING, 1 ERROR. Indexed: no.

This is a data package. Data packages may be large and do not get checked across all platforms.

Target	Result	Time
bioc-checks	NOTE	186
linux-devel	WARNING	871
source / vignettes	ERROR	360
linux-release	WARNING	781

Exports:addHolesToPolygons MouseColonIbdCadinu2024 MouseHypothalamusMoffitt2018 MouseIleumPetukhov2021 plotRasterImage plotTabset plotXY

Dependencies:abind AnnotationDbi AnnotationHub askpass base64enc Biobase BiocBaseUtils BiocFileCache BiocGenerics biocmake BiocManager BiocVersion Biostrings bit bit64 bitops blob bslib BumpyMatrix cachem cli cpp11 crayon curl DBI dbplyr DelayedArray digest dir.expiry dplyr EBImage evaluate ExperimentHub fastmap fftwtools filelock fontawesome fs generics GenomicRanges glue h5mread HDF5Array highr htmltools htmlwidgets httr httr2 IRanges jpeg jquerylib jsonlite KEGGREST knitr lattice lifecycle locfit magick magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig png purrr R6 rappdirs Rcpp RCurl rhdf5 rhdf5filters Rhdf5lib rjson rlang rmarkdown RSQLite S4Arrays S4Vectors sass Seqinfo SingleCellExperiment SparseArray SpatialExperiment stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tiff tinytex utf8 vctrs withr xfun XVector yaml

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Help page	Topics
Collection of public MERFISH datasets	MerfishData-package MerfishData
Add holes to polygons	addHolesToPolygons
MERFISH mouse colon IBD dataset from Cadinu et al., 2024	MouseColonIbdCadinu2024
MERFISH mouse hypothalamus dataset from Moffitt et al., 2018	MouseHypothalamusMoffitt2018
MERFISH mouse ileum dataset from Petukhov et al., 2021	MouseIleumPetukhov2021
Plot raster image	plotRasterImage
Plot a tabset	plotTabset
Plot spatial image with data overlay	plotXY

Package: MerfishData 1.14.1

MerfishData: Collection of public MERFISH datasets

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Help Manual

Usage by other packages (reverse dependencies)