Data

Tools

Indexes

Applications

Experiments

Open Source Science

mudataseurat

.h5mu files interface for Seurat

https://github.com/pmbio/mudataseurat

Science Score: 67.0%

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
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.0%) to scientific vocabulary

Keywords

anndata mudata multi-omics multimodal-omics scrna-seq seurat
Last synced: 6 months ago · JSON representation ·

Repository

.h5mu files interface for Seurat

Basic Info
Statistics
  • Stars: 29
  • Watchers: 10
  • Forks: 13
  • Open Issues: 8
  • Releases: 0
Topics
anndata mudata multi-omics multimodal-omics scrna-seq seurat
Created over 4 years ago · Last pushed about 2 years ago
Metadata Files
Readme Citation

README.md

MuDataSeurat

R-CMD-check pkgdown

Documentation | Preprint | Discord

MuDataSeurat is a package that provides I/O functionality for .h5mu files and Seurat objects.

You can learn more about multimodal data containers in the mudata documentation.

Installation

R remotes::install_github("pmbio/MuDataSeurat")

Quick start

MuDataSeurat provides a set of I/O operations for multimodal data.

MuDataSeurat implements WriteH5MU() that saves Seurat 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 Seurat objects.

MuDataSeurat currently works for Seurat objects of v3 and above.

Writing files

Start with an existing dataset, e.g. a Seurat object with CITE-seq data:

R library(SeuratData) InstallData("bmcite") bm <- LoadData(ds = "bmcite")

WriteH5MU() allows to save the object into a .h5mu file:

R library(MuDataSeurat) WriteH5MU(bm, "bmcite.h5mu")

Please note that only standardised parts of the object are written to the file, and extra information from specific methods, stored in the Seurat object, might be omitted upon writing the file.

Reading files

R bm <- ReadH5MU("bmcite.h5mu")

Please note that only the intersection of cells is currently loaded into the Seurat object due to the object structure limitation. Multimodal embeddings (global .obsm slot) are loaded with the assay.used field set to the default assay. Embeddings names are changed in order to comply with R & Seurat requirements and conventions.

Relevant projects

Other R packages for multimodal I/O include:

Owner

  • Name: Probabilistic Models in Biology
  • Login: PMBio
  • Kind: organization

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: 2
  • Watch event: 6
  • Issue comment event: 4
  • Fork event: 1
Last Year
  • Issues event: 2
  • Watch event: 6
  • Issue comment event: 4
  • Fork event: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 2
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 2
  • Total pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jpark27 (1)
  • maxbond233 (1)
  • mairamirza (1)
  • FlowerPurr (1)
  • maallen3 (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Dependencies

DESCRIPTION cran
  • Matrix * imports
  • Seurat * imports
  • hdf5r * imports
  • methods * imports
  • utils * imports
  • BiocStyle * suggests
  • SeuratData * suggests
  • knitr * suggests
  • rmarkdown * suggests
.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