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MuData

MuData-compatible storage for bioconductor's MultiAssayExperiment

https://github.com/ilia-kats/mudata

Science Score: 77.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: biorxiv.org
  • ✓
    Committers with academic emails
    2 of 5 committers (40.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.5%) to scientific vocabulary

Keywords

anndata bioconductor mudata multi-omics multimodal-omics scrna-seq

Keywords from Contributors

bioconductor-package
Last synced: 6 months ago · JSON representation ·

Repository

MuData-compatible storage for bioconductor's MultiAssayExperiment

Basic Info
Statistics
  • Stars: 6
  • Watchers: 3
  • Forks: 4
  • Open Issues: 2
  • Releases: 0
Topics
anndata bioconductor mudata multi-omics multimodal-omics scrna-seq
Created over 4 years ago · Last pushed 12 months ago
Metadata Files
Readme Changelog Citation

README.md

MuData

R-CMD-check pkgdown

Documentation | Preprint | Discord

MuData is a package that provides I/O functionality 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("ilia-kats/MuData")

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:

Owner

  • Login: ilia-kats
  • Kind: user

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

Total
  • Issues event: 3
  • Watch event: 2
  • Issue comment event: 5
  • Push event: 2
Last Year
  • Issues event: 3
  • Watch event: 2
  • Issue comment event: 5
  • Push event: 2

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 142
  • Total Committers: 5
  • Avg Commits per committer: 28.4
  • Development Distribution Score (DDS): 0.521
Past Year
  • Commits: 3
  • Committers: 2
  • Avg Commits per committer: 1.5
  • Development Distribution Score (DDS): 0.333
Top Committers
Name Email Commits
Ilia Kats i****s@g****t 68
Danila Bredikhin d****n@e****e 61
J Wokaty j****y@s****u 10
Nitesh Turaga n****a@g****m 2
Vito Zanotelli v****i@k****h 1
Committer Domains (Top 20 + Academic)
kispi.uzh.ch: 1 sph.cuny.edu: 1 embl.de: 1 gmx.net: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 6
  • Total pull requests: 4
  • Average time to close issues: 3 months
  • Average time to close pull requests: 2 months
  • Total issue authors: 5
  • Total pull request authors: 3
  • Average comments per issue: 3.83
  • Average comments per pull request: 2.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: 3 months
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 3.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • votti (2)
  • mt1022 (1)
  • A-legac45 (1)
  • multimeric (1)
  • mikelove (1)
Pull Request Authors
  • multimeric (2)
  • votti (1)
  • gtca (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 6,480 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: MuData

Serialization for MultiAssayExperiment Objects

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 6,480 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 14.4%
Stargazers count: 21.8%
Average: 25.8%
Downloads: 93.0%
Maintainers (1)
i.kats@dkfz-heidelberg.de
Last synced: 6 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v2 composite
  • actions/upload-artifact main composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • Matrix * depends
  • S4Vectors * depends
  • rhdf5 >= 2.45 depends
  • DelayedArray * imports
  • MultiAssayExperiment * imports
  • S4Vectors * 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