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README.md
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### Reuse
This project was started with the sole goal of empowering the scientific community to explore and understand their data. As such, we encourage other scientific tool builders in academia or industry to adopt the patterns, tools, and code from this project, and reach out to us with ideas or questions. All code is freely available for reuse under the [MIT license](https://opensource.org/licenses/MIT).
This project was started with the sole goal of empowering the scientific community to explore and understand their data.
As such, we encourage other scientific tool builders in academia or industry to adopt the patterns, tools, and code from
this project. All code is freely available for reuse under the [MIT license](https://opensource.org/licenses/MIT).
Before extending cellxgene, we encourage you to reach out to us with ideas or questions. It might be possible that an
extension could be directly contributed, which would make it available for a wider audience, or that it's on our
[roadmap](./docs/posts/roadmap.md) and under active development.
See the [cellxgene extensions](./docs/posts/extensions.md) section of our documentation for examples of community use and cellxgene extensions.
### Security
docs/_config.yml
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url: posts/roadmap
- title: Contributing (ideas or code)
url: posts/contribute
- title: Extensions
url: posts/extensions
- title: Contact & finding help
url: posts/contact
docs/_site/deprecated/cellxgene_cziscience_com.html
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<!DOCTYPE html>
<html lang="en-US">
<head>
<meta charset="UTF-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<!-- Begin Jekyll SEO tag v2.6.1 -->
<title>cellxgene.cziscience.com | cellxgene</title>
<meta name="generator" content="Jekyll v3.8.7" />
<meta property="og:title" content="cellxgene.cziscience.com" />
<meta property="og:locale" content="en_US" />
<meta name="description" content="An interactive explorer for single-cell transcriptomics data" />
<meta property="og:description" content="An interactive explorer for single-cell transcriptomics data" />
<link rel="canonical" href="https://chanzuckerberg.github.io/cellxgene/deprecated/cellxgene_cziscience_com.html" />
<meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/deprecated/cellxgene_cziscience_com.html" />
<meta property="og:site_name" content="cellxgene" />
<script type="application/ld+json">
{"@type":"WebPage","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"headline":"cellxgene.cziscience.com","description":"An interactive explorer for single-cell transcriptomics data","url":"https://chanzuckerberg.github.io/cellxgene/deprecated/cellxgene_cziscience_com.html","@context":"https://schema.org"}</script>
<!-- End Jekyll SEO tag -->
<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=f70dffced52a32aada1a22504c841e97e941401a">
<!--[if lt IE 9]>
<script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv.min.js"></script>
<![endif]-->
</head>
<body>
<div class="wrapper">
<header>
<img src="/cellxgene/cellxgene-logo.png" alt="cellxgene" />
<p>An interactive explorer for single-cell transcriptomics data</p>
<p>
<a href="/cellxgene/" class="btn">Quick start</a><br>
<a href="/cellxgene/posts/install" class="btn">Installation</a><br>
<a href="/cellxgene/posts/gallery" class="btn">Gallery</a><br>
<a href="/cellxgene/posts/demo-data" class="btn">Demo datasets</a><br>
<a href="https://cellxgene.cziscience.com/" class="btn">All other datasets</a><br>
<a href="/cellxgene/posts/prepare" class="btn">Preparing your data</a><br>
<a href="/cellxgene/posts/launch" class="btn">Launching cellxgene</a><br>
<a href="/cellxgene/posts/hosted" class="btn">Hosting cellxgene</a><br>
<a href="/cellxgene/posts/annotations" class="btn">Annotating data</a><br>
<a href="/cellxgene/posts/methods" class="btn">Methods</a><br>
<a href="/cellxgene/posts/troubleshooting" class="btn">Troubleshooting</a><br>
<a href="/cellxgene/posts/roadmap" class="btn">Roadmap</a><br>
<a href="/cellxgene/posts/contribute" class="btn">Contributing (ideas or code)</a><br>
<a href="/cellxgene/posts/extensions" class="btn">Extensions</a><br>
<a href="/cellxgene/posts/contact" class="btn">Contact & finding help</a><br>
<a href="https://github.com/chanzuckerberg/cellxgene" class="btn" target="_blank">Code</a>
</p>
</header>
<section>
<h1 id="cellxgeneczisciencecom">cellxgene.cziscience.com</h1>
<p>Chan Zuckerberg has an online repository of public single-cell datasets for exploration with cellxgene.</p>
<p>If you have a public dataset which you would like hosted for visualization on this site,
with a link to embed on your own site, please drop us a note at <a href="mailto:cellxgene@chanzuckerberg.com">cellxgene@chanzuckerberg.com</a>.</p>
<table class="fixed-layout">
<thead style="width: 100%">
<tr>
<th>cellxgene link</th>
<th>More Information</th>
</tr>
</thead>
<tbody style="width: 100%">
<tr>
<td><a href="https://cellxgene.cziscience.com/d/krasnow_lab_human_lung_cell_atlas_10x-1.cxg/" target="_blank">Krasnow Lab Human Lung Cell Atlas, 10X</a></td>
<td>
<a href="http://cmgm-new.stanford.edu/krasnow/">Krasnow Lab</a>,
<a href="https://github.com/krasnowlab/hlca">HLCA website</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/krasnow_lab_human_lung_cell_atlas_smartseq2-2.cxg/" target="_blank">Krasnow Lab Human Lung Cell Atlas, Smart-seq2</a></td>
<td>
<a href="http://cmgm-new.stanford.edu/krasnow/">Krasnow Lab</a>,
<a href="https://github.com/krasnowlab/hlca">HLCA website</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/human_cell_landscape-3.cxg/" target="_blank">Human Cell Landscape</a></td>
<td>
<a href="https://person.zju.edu.cn/en/ggj">Guo Lab</a>,
<a href="http://bis.zju.edu.cn/HCL/">HCL website</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/human_fetal_liver_single_cell_transcriptome-13.cxg/" target="_blank">Human fetal liver single cell transcriptome data</a></td>
<td>
<a href="https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-7407/">E-MTAB-7407</a>,
<a href="https://www.covid19cellatlas.org/">covid19cellatlas.org</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/cell_atlas_of_thymic_development-14.cxg/" target="_blank">A cell atlas of human thymic development defines T cell repertoire formation</a></td>
<td>
<a href="https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-8581/">E-MTAB-8581</a>,
<a href="https://www.covid19cellatlas.org/">covid19cellatlas.org</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/cellular_census_of_human_lungs_alveoli_and_parenchyma-15.cxg/" target="_blank">A cellular census of human lungs identifies novel cell states in health and in asthma - parenchyma</a></td>
<td>
<a href="https://asthma.cellgeni.sanger.ac.uk/">asthma.cellgeni.sanger.ac.uk</a>,
<a href="https://www.covid19cellatlas.org/">covid19cellatlas.org</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/cellular_census_of_human_lungs_nasal-16.cxg/" target="_blank">A cellular census of human lungs identifies novel cell states in health and in asthma - nasal</a></td>
<td>
<a href="https://asthma.cellgeni.sanger.ac.uk/">asthma.cellgeni.sanger.ac.uk</a>,
<a href="https://www.covid19cellatlas.org/">covid19cellatlas.org</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/cellular_census_of_human_lungs_bronchi-17.cxg/" target="_blank">A cellular census of human lungs identifies novel cell states in health and in asthma - bronchi</a></td>
<td>
<a href="https://asthma.cellgeni.sanger.ac.uk/">asthma.cellgeni.sanger.ac.uk</a>,
<a href="https://www.covid19cellatlas.org/">covid19cellatlas.org</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/ischaemic_sensitivity_of_human_tissue_by_single_cell_RNA_seq_lung-18.cxg/" target="_blank">Ischaemic sensitivity of human tissue by single cell RNA seq - lung</a></td>
<td>
<a href="https://data.humancellatlas.org/explore/projects/c4077b3c-5c98-4d26-a614-246d12c2e5d7">HCA</a>,
<a href="https://www.covid19cellatlas.org/">covid19cellatlas.org</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/ischaemic_sensitivity_of_human_tissue_by_single_cell_RNA_seq_spleen-19.cxg/" target="_blank">Ischaemic sensitivity of human tissue by single cell RNA seq - spleen</a></td>
<td>
<a href="https://data.humancellatlas.org/explore/projects/c4077b3c-5c98-4d26-a614-246d12c2e5d7">HCA</a>,
<a href="https://www.covid19cellatlas.org/">covid19cellatlas.org</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/ischaemic_sensitivity_of_human_tissue_by_single_cell_RNA_seq_oesophagus-20.cxg/" target="_blank">Ischaemic sensitivity of human tissue by single cell RNA seq - oesophagus</a></td>
<td>
<a href="https://data.humancellatlas.org/explore/projects/c4077b3c-5c98-4d26-a614-246d12c2e5d7">HCA</a>,
<a href="https://www.covid19cellatlas.org/">covid19cellatlas.org</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/spatio_temporal_immune_zonation_of_the_human_kidney-21.cxg/" target="_blank">Spatio-temporal immune zonation of the human kidney</a></td>
<td>
<a href="https://www.kidneycellatlas.org/">www.kidneycellatlas.org</a>,
<a href="https://www.covid19cellatlas.org/">covid19cellatlas.org</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/fetal_maternal_interface_10x-22.cxg/" target="_blank">Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics - 10x</a></td>
<td>
<a href="https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6701/">E-MTAB-6701</a>,
<a href="https://www.covid19cellatlas.org/">covid19cellatlas.org</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/fetal_maternal_interface_smartseq2-23.cxg/" target="_blank">Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics - SmartSeq2</a></td>
<td>
<a href="https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6701/">E-MTAB-6701</a>,
<a href="https://www.covid19cellatlas.org/">covid19cellatlas.org</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/gut_cell_atlas-24.cxg/" target="_blank">Gut Cell Atlas</a></td>
<td>
<a href="https://www.gutcellatlas.org/">www.gutcellatlas.org</a>,
<a href="https://www.covid19cellatlas.org/">covid19cellatlas.org</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/Single_cell_atlas_of_peripheral_immune_response_to_SARS_CoV_2_infection-25.cxg/" target="_blank">A single-cell atlas of the peripheral immune response to severe COVID-19</a></td>
<td>
<a href="https://blishlab.sites.stanford.edu/">Blish Lab</a>,
<a href="https://www.medrxiv.org/content/10.1101/2020.04.17.20069930v1">medRxiv preprint</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/Atlas_of_Healthy_and_SHIV_Infected_Non_Human_Primate_Lung_and_Ileum_ACE2+_Cells_ileum-12.cxg/" target="_blank">Atlas of Healthy and SHIV-Infected Non-Human Primate Lung and Ileum ACE2+ Cells - Ileum</a></td>
<td>
<a href="https://singlecell.broadinstitute.org/single_cell/study/SCP807/atlas-of-healthy-and-shiv-infected-non-human-primate-lung-and-ileum-ace2-cells?scpbr=the-alexandria-project">Single Cell Portal</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/Atlas_of_Healthy_and_SHIV_Infected_Non_Human_Primate_Lung_and_Ileum_ACE2+_Cells_lung-11.cxg/" target="_blank">Atlas of Healthy and SHIV-Infected Non-Human Primate Lung and Ileum ACE2+ Cells - Lung</a></td>
<td>
<a href="https://singlecell.broadinstitute.org/single_cell/study/SCP807/atlas-of-healthy-and-shiv-infected-non-human-primate-lung-and-ileum-ace2-cells?scpbr=the-alexandria-project">Single Cell Portal</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/Allergic_inflammatory_memory_in_human_respiratory_epithelial_progenitor_cells_epithelial-10.cxg/" target="_blank">Allergic inflammatory memory in human respiratory epithelial progenitor cells - epithelial cells</a></td>
<td>
<a href="https://singlecell.broadinstitute.org/single_cell/study/SCP253/allergic-inflammatory-memory-in-human-respiratory-epithelial-progenitor-cells?scpbr=the-alexandria-project">Single Cell Portal</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/Allergic_inflammatory_memory_in_human_respiratory_epithelial_progenitor_cells_scraping-9.cxg/" target="_blank">Allergic inflammatory memory in human respiratory epithelial progenitor cells - nasal scrapings</a></td>
<td>
<a href="https://singlecell.broadinstitute.org/single_cell/study/SCP253/allergic-inflammatory-memory-in-human-respiratory-epithelial-progenitor-cells?scpbr=the-alexandria-project">Single Cell Portal</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/Allergic_inflammatory_memory_in_human_respiratory_epithelial_progenitor_cells_surgical-8.cxg/" target="_blank">Allergic inflammatory memory in human respiratory epithelial progenitor cells - surgical</a></td>
<td>
<a href="https://singlecell.broadinstitute.org/single_cell/study/SCP253/allergic-inflammatory-memory-in-human-respiratory-epithelial-progenitor-cells?scpbr=the-alexandria-project">Single Cell Portal</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/Allergic_inflammatory_memory_in_human_respiratory_epithelial_progenitor_cells_nasalsss-26.cxg/" target="_blank">Allergic inflammatory memory in human respiratory epithelial progenitor cells - nasal SSS</a></td>
<td>
<a href="https://singlecell.broadinstitute.org/single_cell/study/SCP253/allergic-inflammatory-memory-in-human-respiratory-epithelial-progenitor-cells?scpbr=the-alexandria-project">Single Cell Portal</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/ACE2_and_TMPRSS2_expression_in_human_non_inflamed_terminal_ileum_epithelial-7.cxg/" target="_blank">ACE2 and TMPRSS2 expression in human non-inflamed terminal ileum - epithelial cells</a></td>
<td>
<a href="https://singlecell.broadinstitute.org/single_cell/study/SCP812/ace2-and-tmprss2-expression-in-human-non-inflamed-terminal-ileum?scpbr=the-alexandria-project">Single Cell Portal</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/ACE2_and_TMPRSS2_expression_in_human_non_inflamed_terminal_ileum-6.cxg/" target="_blank">ACE2 and TMPRSS2 expression in human non-inflamed terminal ileum</a></td>
<td>
<a href="https://singlecell.broadinstitute.org/single_cell/study/SCP812/ace2-and-tmprss2-expression-in-human-non-inflamed-terminal-ileum?scpbr=the-alexandria-project">Single Cell Portal</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/Human_Lung_HIV_TB_Co_infection_ACE2+_Cells-5.cxg/" target="_blank">Human Lung HIV-TB Co-infection ACE2+ Cells</a></td>
<td>
<a href="https://singlecell.broadinstitute.org/single_cell/study/SCP814/human-lung-hiv-tb-co-infection-ace2-cells?scpbr=the-alexandria-project">Single Cell Portal</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/Epithelial_Cells_in_NHP_mTB_Granuloma_and_Uninvolved_Lung-4.cxg/" target="_blank">Epithelial Cells in NHP mTB Granuloma and Uninvolved Lung</a></td>
<td>
<a href="https://singlecell.broadinstitute.org/single_cell/study/SCP806/epithelial-cells-in-nhp-mtb-granuloma-and-uninvolved-lung?scpbr=the-alexandria-project">Single Cell Portal</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/kampmann_lab_human_AD_snRNAseq_EC-49.cxg/
" target="_blank">Selective Neuronal Vulnerability in Alzheimer's Disease</a></td>
<td>
<a href="https://kampmannlab.ucsf.edu/">Kampmann Lab</a>,
<a href="https://www.biorxiv.org/content/10.1101/2020.04.04.025825v2">BioRxiv preprint</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/kampmann_lab_human_AD_snRNAseq_SFG-50.cxg/
" target="_blank">Selective Neuronal Vulnerability in Alzheimer's Disease: Superior Frontal Gyrus</a></td>
<td>
<a href="https://kampmannlab.ucsf.edu/">Kampmann Lab</a>,
<a href="https://www.biorxiv.org/content/10.1101/2020.04.04.025825v2">BioRxiv preprint</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/kampmann_lab_human_AD_snRNAseq_EC_astrocytes-51.cxg/
" target="_blank">Selective Neuronal Vulnerability in Alzheimer's Disease: Astrocytes in EC</a></td>
<td>
<a href="https://kampmannlab.ucsf.edu/">Kampmann Lab</a>,
<a href="https://www.biorxiv.org/content/10.1101/2020.04.04.025825v2">BioRxiv preprint</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/kampmann_lab_human_AD_snRNAseq_EC_excitatoryNeurons-52.cxg/
" target="_blank">Selective Neuronal Vulnerability in Alzheimer's Disease: Excitatory Neurons in EC</a></td>
<td>
<a href="https://kampmannlab.ucsf.edu/">Kampmann Lab</a>,
<a href="https://www.biorxiv.org/content/10.1101/2020.04.04.025825v2">BioRxiv preprint</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/kampmann_lab_human_AD_snRNAseq_EC_inhibitoryNeurons-53.cxg/
" target="_blank">Selective Neuronal Vulnerability in Alzheimer's Disease: Inhibitory Neurons in EC</a></td>
<td>
<a href="https://kampmannlab.ucsf.edu/">Kampmann Lab</a>,
<a href="https://www.biorxiv.org/content/10.1101/2020.04.04.025825v2">BioRxiv preprint</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/kampmann_lab_human_AD_snRNAseq_EC_microglia-54.cxg/
" target="_blank">Selective Neuronal Vulnerability in Alzheimer's Disease: Microglia in EC</a></td>
<td>
<a href="https://kampmannlab.ucsf.edu/">Kampmann Lab</a>,
<a href="https://www.biorxiv.org/content/10.1101/2020.04.04.025825v2">BioRxiv preprint</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/kampmann_lab_human_AD_snRNAseq_SFG_astrocytes-55.cxg/
" target="_blank">Selective Neuronal Vulnerability in Alzheimer's Disease: Astrocytes in SFG</a></td>
<td>
<a href="https://kampmannlab.ucsf.edu/">Kampmann Lab</a>,
<a href="https://www.biorxiv.org/content/10.1101/2020.04.04.025825v2">BioRxiv preprint</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/kampmann_lab_human_AD_snRNAseq_SFG_excitatoryNeurons-56.cxg/
" target="_blank">Selective Neuronal Vulnerability in Alzheimer's Disease: Excitatory Neurons in SFG</a></td>
<td>
<a href="https://kampmannlab.ucsf.edu/">Kampmann Lab</a>,
<a href="https://www.biorxiv.org/content/10.1101/2020.04.04.025825v2">BioRxiv preprint</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/kampmann_lab_human_AD_snRNAseq_SFG_inhibitoryNeurons-57.cxg/" target="_blank">Selective Neuronal Vulnerability in Alzheimer's Disease: Inhibitory Neurons in SFG</a></td>
<td>
<a href="https://kampmannlab.ucsf.edu/">Kampmann Lab</a>,
<a href="https://www.biorxiv.org/content/10.1101/2020.04.04.025825v2">BioRxiv preprint</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/kampmann_lab_human_AD_snRNAseq_SFG_microglia-58.cxg/" target="_blank">Selective Neuronal Vulnerability in Alzheimer's Disease: Microglia in SFG</a></td>
<td>
<a href="https://kampmannlab.ucsf.edu/">Kampmann Lab</a>,
<a href="https://www.biorxiv.org/content/10.1101/2020.04.04.025825v2">BioRxiv preprint</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/Single_cell_gene_expression_profiling_of_SARS_CoV_2_infected_human_cell_lines_H1299-27.cxg/" target="_blank">Single-cell gene expression profiling of SARS-CoV-2 infected human cell lines - H1299</a></td>
<td>
<a href="https://www.mdc-berlin.de/landthaler#t-single-cellsars-cov-2">Landthaler Lab</a>,
<a href="https://www.biorxiv.org/content/10.1101/2020.05.05.079194v1">BioRxiv preprint</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/Single_cell_gene_expression_profiling_of_SARS_CoV_2_infected_human_cell_lines_Calu_3-28.cxg/" target="_blank">Single-cell gene expression profiling of SARS-CoV-2 infected human cell lines - Calu-3</a></td>
<td>
<a href="https://www.mdc-berlin.de/landthaler#t-single-cellsars-cov-2">Landthaler Lab</a>,
<a href="https://www.biorxiv.org/content/10.1101/2020.05.05.079194v1">BioRxiv preprint</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/Single_cell_drug_screening_a549-42.cxg/" target="_blank">Single-cell drug screening - A549</a></td>
<td>
<a href="https://github.com/cole-trapnell-lab/sci-plex">Trapnell Lab Github</a>,
<a href="https://science.sciencemag.org/content/367/6473/45">Science</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/Single_cell_drug_screening_k562-43.cxg/" target="_blank">Single-cell drug screening - K562</a></td>
<td>
<a href="https://github.com/cole-trapnell-lab/sci-plex">Trapnell Lab Github</a>,
<a href="https://science.sciencemag.org/content/367/6473/45">Science</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/Single_cell_drug_screening_mcf7-44.cxg/" target="_blank">Single-cell drug screening - MCF7</a></td>
<td>
<a href="https://github.com/cole-trapnell-lab/sci-plex">Trapnell Lab Github</a>,
<a href="https://science.sciencemag.org/content/367/6473/45">Science</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.prod.single-cell.czi.technology/d/Molecular_atlas_of_cell_types_and_zonation_in_the_brain_vasculature-48.cxg/" target="_blank">A molecular atlas of cell types and zonation in the brain vasculature</a></td>
<td>
<a href="http://betsholtzlab.org/VascularSingleCells/database.html">Betsholtz Lab</a>,
<a href="https://www.nature.com/articles/nature25739">Nature</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/Single_soma_transcriptomics_AT8-45.cxg/" target="_blank">Single Soma Transcriptomics - AT8</a></td>
<td>
<a href="https://www.biorxiv.org/content/10.1101/2020.05.11.088591v1">bioRxiv preprint</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/Single_soma_transcriptomics_MAP2-46.cxg/" target="_blank">Single Soma Transcriptomics - MAP2</a></td>
<td>
<a href="https://www.biorxiv.org/content/10.1101/2020.05.11.088591v1">bioRxiv preprint</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/Single_soma_transcriptomics_MAP2AT8-47.cxg/" target="_blank">Single Soma Transcriptomics - MAP2AT8</a></td>
<td>
<a href="https://www.biorxiv.org/content/10.1101/2020.05.11.088591v1">bioRxiv preprint</a>
</td>
</tr>
<tr>
<td><a href="https://cellxgene.cziscience.com/d/Single_cell_longitudinal_analysis_of_SARS_CoV_2_infection_in_human_bronchial_epithelial_cells-29.cxg/" target="_blank">Single-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cells</a></td>
<td>
<a href="https://www.biorxiv.org/content/10.1101/2020.05.06.081695v2">bioRxiv preprint</a>
</td>
</tr>
</tbody>
</table>
</section>
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<a href="/cellxgene/posts/extensions" class="btn">Extensions</a><br>
<a href="/cellxgene/posts/contact" class="btn">Contact & finding help</a><br>
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<p>An interactive explorer for single-cell transcriptomics data</p>
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<a href="/cellxgene/" class="btn">Quick start</a><br>
<a href="/cellxgene/posts/install" class="btn">Installation</a><br>
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<a href="https://cellxgene.cziscience.com/" class="btn">All other datasets</a><br>
<a href="/cellxgene/posts/prepare" class="btn">Preparing your data</a><br>
<a href="/cellxgene/posts/launch" class="btn">Launching cellxgene</a><br>
<a href="/cellxgene/posts/hosted" class="btn">Hosting cellxgene</a><br>
<a href="/cellxgene/posts/annotations" class="btn">Annotating data</a><br>
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<section>
<h1 id="extensions">Extensions</h1>
<p>This project was started with the sole goal of empowering the scientific community to explore and understand their data.
As such, we encourage other scientific tool builders in academia or industry to adopt the patterns, tools, and code from
this project. All code is freely available for reuse under the <a href="https://opensource.org/licenses/MIT">MIT license</a>.</p>
<p>Before extending cellxgene, we encourage you to reach out to us with ideas or questions. It might be possible that an
extension could be directly contributed, which would make it available for a wider audience, or that it’s on our
<a href="/cellxgene/posts/roadmap.html">roadmap</a> and under active development.</p>
<p>Please note that cellxgene does not have public APIs. Our development may break extensions. We will document changes to the code base but it is advised that extensions pin the version of cellxgene they develop against.</p>
<h2 id="example-reuse--extensions">Example Reuse &amp; extensions</h2>
<h4 id="cellxgene-gateway">cellxgene Gateway</h4>
<p><a href="https://github.com/Novartis/cellxgene-gateway">cellxgene Gateway</a> allows you to use with multiple datasets. It
displays an index of available h5ad (anndata) files. When a user clicks on a file name, it launches a Cellxgene Server
instance that loads that particular data file and once it is available proxies requests to that server.</p>
<h4 id="cellxgene-vip-visualization-in-plugin">cellxgene-VIP (Visualization in Plugin)</h4>
<p><a href="https://github.com/interactivereport/cellxgene_VIP">cellxgene-VIP</a> enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.</p>
<h4 id="galaxy">Galaxy</h4>
<p><a href="https://singlecell.usegalaxy.eu/">Galaxy</a> is an open source, web-based platform for data intensive biomedical research. cellxgene can be accessed within Galaxy to view analyzed datasets.
See also the relevant <a href="https://www.biorxiv.org/content/10.1101/2020.06.06.137570v1.full.pdf">publication</a></p>
<h4 id="single-cell-portal">Single Cell Portal</h4>
<p>The <a href="https://singlecell.broadinstitute.org/single_cell">Single Cell Portal</a> is a data hosting and visualization service. cellxgene can be embedded as an additional view to complement the visualizations provided by the.
<a href="https://singlecell.broadinstitute.org/single_cell/study/SCP807/atlas-of-healthy-and-shiv-infected-non-human-primate-lung-and-ileum-ace2-cells">Example</a>.</p>
<h4 id="fastgenomics">FASTGenomics</h4>
<p><a href="https://beta.fastgenomics.org/">FASTGenomics</a> is a collaborative research platform that offers easy-to-use data management and reproducible analytics to drive single-cell research forward. Many of the publicly available datasets in FASTGenomics - as well as your private datasets - can be interactively explored with cellxgene.
See also this <a href="https://beta.fastgenomics.org/datasets/detail-dataset-952687f71ef34322a850553c4a24e82e#Cellxgene">example</a> for data from <a href="https://beta.fastgenomics.org/p/schulte-schrepping_covid19">Schulte-Schrepping et al. (Cell, 2020)</a>.
Note that it is not necessary to create an account, anonymous login is permitted.</p>
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# Extensions
This project was started with the sole goal of empowering the scientific community to explore and understand their data.
As such, we encourage other scientific tool builders in academia or industry to adopt the patterns, tools, and code from
this project. All code is freely available for reuse under the [MIT license](https://opensource.org/licenses/MIT).
Before extending cellxgene, we encourage you to reach out to us with ideas or questions. It might be possible that an
extension could be directly contributed, which would make it available for a wider audience, or that it's on our
[roadmap](./roadmap.md) and under active development.
Please note that cellxgene does not have public APIs. Our development may break extensions. We will document changes to the code base but it is advised that extensions pin the version of cellxgene they develop against.
## Example Reuse & extensions
#### cellxgene Gateway
[cellxgene Gateway](https://github.com/Novartis/cellxgene-gateway) allows you to use with multiple datasets. It
displays an index of available h5ad (anndata) files. When a user clicks on a file name, it launches a Cellxgene Server
instance that loads that particular data file and once it is available proxies requests to that server.
#### cellxgene-VIP (Visualization in Plugin)
[cellxgene-VIP](https://github.com/interactivereport/cellxgene_VIP) enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.
#### Galaxy
[Galaxy](https://singlecell.usegalaxy.eu/) is an open source, web-based platform for data intensive biomedical research. cellxgene can be accessed within Galaxy to view analyzed datasets.
See also the relevant [publication](https://www.biorxiv.org/content/10.1101/2020.06.06.137570v1.full.pdf)
#### Single Cell Portal
The [Single Cell Portal](https://singlecell.broadinstitute.org/single_cell) is a data hosting and visualization service. cellxgene can be embedded as an additional view to complement the visualizations provided by the.
[Example](https://singlecell.broadinstitute.org/single_cell/study/SCP807/atlas-of-healthy-and-shiv-infected-non-human-primate-lung-and-ileum-ace2-cells).
#### FASTGenomics
[FASTGenomics](https://beta.fastgenomics.org/) is a collaborative research platform that offers easy-to-use data management and reproducible analytics to drive single-cell research forward. Many of the publicly available datasets in FASTGenomics - as well as your private datasets - can be interactively explored with cellxgene.
See also this [example](https://beta.fastgenomics.org/datasets/detail-dataset-952687f71ef34322a850553c4a24e82e#Cellxgene) for data from [Schulte-Schrepping et al. (Cell, 2020)](https://beta.fastgenomics.org/p/schulte-schrepping_covid19).
Note that it is not necessary to create an account, anonymous login is permitted.
docs/posts/extensions.md
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@@ -0,0 +1,39 @@
# Extensions
This project was started with the sole goal of empowering the scientific community to explore and understand their data.
As such, we encourage other scientific tool builders in academia or industry to adopt the patterns, tools, and code from
this project. All code is freely available for reuse under the [MIT license](https://opensource.org/licenses/MIT).
Before extending cellxgene, we encourage you to reach out to us with ideas or questions. It might be possible that an
extension could be directly contributed, which would make it available for a wider audience, or that it's on our
[roadmap](./roadmap.md) and under active development.
Please note that cellxgene does not have public APIs. Our development may break extensions. We will document changes to the code base but it is advised that extensions pin the version of cellxgene they develop against.
## Example Reuse & extensions
#### cellxgene Gateway
[cellxgene Gateway](https://github.com/Novartis/cellxgene-gateway) allows you to use with multiple datasets. It
displays an index of available h5ad (anndata) files. When a user clicks on a file name, it launches a Cellxgene Server
instance that loads that particular data file and once it is available proxies requests to that server.
#### cellxgene-VIP (Visualization in Plugin)
[cellxgene-VIP](https://github.com/interactivereport/cellxgene_VIP) enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.
#### Galaxy
[Galaxy](https://singlecell.usegalaxy.eu/) is an open source, web-based platform for data intensive biomedical research. cellxgene can be accessed within Galaxy to view analyzed datasets.
See also the relevant [publication](https://www.biorxiv.org/content/10.1101/2020.06.06.137570v1.full.pdf)
#### Single Cell Portal
The [Single Cell Portal](https://singlecell.broadinstitute.org/single_cell) is a data hosting and visualization service. cellxgene can be embedded as an additional view to complement the visualizations provided by the.
[Example](https://singlecell.broadinstitute.org/single_cell/study/SCP807/atlas-of-healthy-and-shiv-infected-non-human-primate-lung-and-ileum-ace2-cells).
#### FASTGenomics
[FASTGenomics](https://beta.fastgenomics.org/) is a collaborative research platform that offers easy-to-use data management and reproducible analytics to drive single-cell research forward. Many of the publicly available datasets in FASTGenomics - as well as your private datasets - can be interactively explored with cellxgene.
See also this [example](https://beta.fastgenomics.org/datasets/detail-dataset-952687f71ef34322a850553c4a24e82e#Cellxgene) for data from [Schulte-Schrepping et al. (Cell, 2020)](https://beta.fastgenomics.org/p/schulte-schrepping_covid19).
Note that it is not necessary to create an account, anonymous login is permitted.