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GitHub / nf-core / spatialvi

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fspatialvi

Stars: 39
Forks: 12
Open Issues: 6

License: mit
Language: Nextflow
Repo Size: 6.96 MB
Dependencies: 31

Created: about 2 years ago
Updated: about 2 hours ago
Last pushed: about 3 hours ago
Last synced: about 2 hours ago

Commit Stats

Commits: 384
Authors: 13
Mean commits per author: 29.54
Development Distribution Score: 0.424
More commit stats: https://commits.ecosyste.ms/hosts/GitHub/repositories/nf-core/spatialvi

Topics: 10x-genomics, 10xgenomics, bioinformatics, image-processing, microscopy, nextflow, nf-core, pipeline, rna-seq, single-cell, spatial, spatial-transcriptomics, st, transcriptomics, visium, workflow

Files
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    Readme
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    Dependencies
    .github/workflows/awsfulltest.yml actions
    .github/workflows/awstest.yml actions
    .github/workflows/branch.yml actions
    .github/workflows/ci.yml actions
    .github/workflows/linting.yml actions
    .github/workflows/linting_comment.yml actions
    .github/workflows/clean-up.yml actions
    .github/workflows/fix-linting.yml actions
    modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan
    modules/nf-core/fastqc/meta.yml cpan
    modules/nf-core/multiqc/meta.yml cpan
    modules/nf-core/spaceranger/count/meta.yml cpan
    modules/nf-core/untar/meta.yml cpan
    env/reports/Dockerfile docker
    pyproject.toml pypi
    .github/workflows/release-announcements.yml actions
    .github/workflows/download_pipeline.yml actions
    modules/nf-core/custom/dumpsoftwareversions/environment.yml conda
    modules/nf-core/fastqc/environment.yml conda
    modules/nf-core/multiqc/environment.yml conda
    modules/nf-core/untar/environment.yml conda
    env/reports/environment.yml pypi
    env/st_spatial_de/environment.yml pypi