Science Score: 67.0%
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○Scientific vocabulary similarity
Low similarity (11.1%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- Language: R
- Default Branch: devel
- Size: 120 KB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
MuData
Documentation | Preprint | Discord
MuData is a package that provides I/O funcitonality for .h5mu files and MultiAssayExperiment objects.
You can learn more about multimodal data containers in the reference mudata documentation.
Installation
MuData uses rhdf5 to access .h5mu and .h5ad files. In the meantime, the bioc-devel version of rhdf5 must be used.
rhdf5 and MuData can be installed by running
R
remotes::install_github("grimbough/rhdf5")
remotes::install_github("pmbio/MuDataMAE")
We use rhdf5 over hdf5r to stay compatible with the rest of the Bioconductor ecosystem.
In particular, using hdf5r would make integrating with other packages building on rhdf5, such as HDF5Array, much more difficult, if not impossible. We have implemented necessary HDF5 features that the .h5ad and consequently .h5mu formats make use of upstream, including file creation properties and object references.
Quick start
MuData provides a set of I/O operations for multimodal data.
MuData implements WriteH5MU() that saves MultiAssayExperiment objects to .h5mu files that can be further integrated into workflows in multiple programming languages, including the muon Python library and the Muon.jl Julia library. ReadH5MU() reads .h5mu files into MultiAssayExperiment objects.
Writing files
Start with an existing dataset, e.g. a MultiAssayExperiment object with five distinct modalities:
R
library(MultiAssayExperiment)
data(miniACC)
WriteH5MU() allows to save the object into a .h5mu file:
R
library(MuData)
WriteH5MU(miniACC, "miniACC.h5mu")
Reading files
R
miniACC <- ReadH5MU("miniACC.h5mu")
Relevant projects
Other R packages for multimodal I/O include:
- MuDataSeurat for Seurat objects
- SeuratDisk
Owner
- Name: (WIP DEV) Bioconductor Packages
- Login: bioconductor-source
- Kind: organization
- Email: maintainer@bioconductor.org
- Website: https://bioconductor.org
- Repositories: 1
- Profile: https://github.com/bioconductor-source
Source code for packages accepted into Bioconductor
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Bredikhin"
given-names: "Danila"
orcid: "https://orcid.org/0000-0001-8089-6983"
- family-names: "Kats"
given-names: "Ilia"
orcid: "https://orcid.org/0000-0001-5220-5671"
title: "muon"
version: 1.0.0
date-released: 2021-06-01
url: "https://github.com/scverse/muon"
preferred-citation:
type: article
authors:
- family-names: "Bredikhin"
given-names: "Danila"
orcid: "https://orcid.org/0000-0001-8089-6983"
- family-names: "Kats"
given-names: "Ilia"
orcid: "https://orcid.org/0000-0001-5220-5671"
- family-names: "Stegle"
given-names: "Oliver"
orcid: "https://orcid.org/0000-0002-8818-7193"
doi: "10.1186/s13059-021-02577-8"
journal: "Genome Biology"
month: 2
title: "MUON: multimodal omics analysis framework"
year: 2022
GitHub Events
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Dependencies
- actions/checkout v2 composite
- actions/upload-artifact main composite
- r-lib/actions/check-r-package v1 composite
- r-lib/actions/setup-pandoc v1 composite
- r-lib/actions/setup-r v1 composite
- r-lib/actions/setup-r-dependencies v1 composite
- actions/checkout v2 composite
- r-lib/actions/setup-pandoc v1 composite
- r-lib/actions/setup-r v1 composite
- r-lib/actions/setup-r-dependencies v1 composite
- Matrix * depends
- S4Vectors * depends
- rhdf5 * depends
- DelayedArray * imports
- MultiAssayExperiment * imports
- SingleCellExperiment * imports
- SummarizedExperiment * imports
- methods * imports
- stats * imports
- BiocStyle * suggests
- CiteFuse * suggests
- HDF5Array * suggests
- SingleCellMultiModal * suggests
- covr * suggests
- fs * suggests
- knitr * suggests
- rmarkdown * suggests
- scater * suggests
- testthat * suggests