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parashardhapola / scarf

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.
http://scarf.readthedocs.io
BSD 3-Clause "New" or "Revised" License
96 stars 12 forks source link
big-data bioinformatics cite-seq clustering differential-expression dimension-reduction gene-modules genomics graph-analytics memory-efficient multiomics pseudotime scalable-data-analysis scatac-seq scrna-seq single-cell-atac-seq single-cell-genomics single-cell-rna-seq tsne umap

readme

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                <a href="https://github.com/parashardhapola/scarf">
                     <img src="https://rawcdn.githack.com/parashardhapola/scarf/eefd75a0893a8903b8fcf8c51b5e7cb8e672a272/docs/source/logo_wide.png" alt="Scarf logo" width="600px" />
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                <h3>A framework for memory-efficient analysis of single-cell genomics data</h3>
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           <a href="https://pypi.org/project/scarf">
                <img src="https://img.shields.io/pypi/v/scarf.svg" alt="PyPiVersion" />
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           <a href="https://scarf.readthedocs.io">
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                <img src="https://github.com/parashardhapola/scarf/actions/workflows/pytest.yml/badge.svg" alt="TestStatus" />
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           <a href="https://github.com/psf/black">
                <img src="https://img.shields.io/badge/code%20style-black-000000.svg" alt="GitHub tweet" />
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           <a href="https://scarf.readthedocs.io/en/latest/install.html"> šŸ”Œ Installation</a> |
           <a href="http://scarf.rtfd.io"> šŸ“– Documentation</a> |
           <a href="https://scarf.readthedocs.io/en/latest/vignettes/basic_tutorial_scRNAseq.html"> šŸš€ Getting started</a> |
           <a href="https://www.nature.com/articles/s41467-022-32097-3">šŸ“ Article in Nature Comm</a>
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           Install with all the dependencies:
           <code style="background-color: #F0F0F0; padding: 2px 4px; border-radius: 4px; font-family: monospace;">pip install scarf[extra]</code>
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           <strong>Need support?</strong> Create an issue <a href="https://github.com/parashardhapola/scarf/issues">on Github</a>.
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