From e264724597476aab631715cad1d96e9acd6f4521 Mon Sep 17 00:00:00 2001 From: Ambrose J Carr Date: Tue, 12 Jan 2021 08:55:14 -0500 Subject: [PATCH] Add extension showcase to documentation (#1878) --- README.md | 11 +- docs/_config.yml | 2 + .../deprecated/cellxgene_cziscience_com.html | 446 ++++++++++++++++++ docs/_site/index.html | 10 +- docs/_site/posts/extensions.html | 152 ++++++ docs/_site/posts/extensions.md | 39 ++ docs/posts/extensions.md | 39 ++ 7 files changed, 695 insertions(+), 4 deletions(-) create mode 100644 docs/_site/deprecated/cellxgene_cziscience_com.html create mode 100644 docs/_site/posts/extensions.html create mode 100644 docs/_site/posts/extensions.md create mode 100644 docs/posts/extensions.md diff --git a/README.md b/README.md index 669d2675..cec1258d 100644 --- a/README.md +++ b/README.md @@ -73,7 +73,16 @@ This project adheres to the Contributor Covenant [code of conduct](https://githu ### 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 diff --git a/docs/_config.yml b/docs/_config.yml index 6e29ea64..4290ac5f 100644 --- a/docs/_config.yml +++ b/docs/_config.yml @@ -33,5 +33,7 @@ nav: url: posts/roadmap - title: Contributing (ideas or code) url: posts/contribute + - title: Extensions + url: posts/extensions - title: Contact & finding help url: posts/contact diff --git a/docs/_site/deprecated/cellxgene_cziscience_com.html b/docs/_site/deprecated/cellxgene_cziscience_com.html new file mode 100644 index 00000000..f23a54b0 --- /dev/null +++ b/docs/_site/deprecated/cellxgene_cziscience_com.html @@ -0,0 +1,446 @@ + + + + + + + + +cellxgene.cziscience.com | cellxgene + + + + + + + + + + + + + + + +
+
+ cellxgene + +

An interactive explorer for single-cell transcriptomics data

+

+ + + Quick start
+ + + + + Installation
+ + + + Gallery
+ + + + Demo datasets
+ + + + All other datasets
+ + + + Preparing your data
+ + + + Launching cellxgene
+ + + + Hosting cellxgene
+ + + + Annotating data
+ + + + Methods
+ + + + Troubleshooting
+ + + + Roadmap
+ + + + Contributing (ideas or code)
+ + + + Extensions
+ + + + Contact & finding help
+ + + + Code +

+
+ +
+

cellxgene.cziscience.com

+ +

Chan Zuckerberg has an online repository of public single-cell datasets for exploration with cellxgene.

+ +

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 cellxgene@chanzuckerberg.com.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
cellxgene linkMore Information
Krasnow Lab Human Lung Cell Atlas, 10X + Krasnow Lab, + HLCA website +
Krasnow Lab Human Lung Cell Atlas, Smart-seq2 + Krasnow Lab, + HLCA website +
Human Cell Landscape + Guo Lab, + HCL website +
Human fetal liver single cell transcriptome data + E-MTAB-7407, + covid19cellatlas.org +
A cell atlas of human thymic development defines T cell repertoire formation + E-MTAB-8581, + covid19cellatlas.org +
A cellular census of human lungs identifies novel cell states in health and in asthma - parenchyma + asthma.cellgeni.sanger.ac.uk, + covid19cellatlas.org +
A cellular census of human lungs identifies novel cell states in health and in asthma - nasal + asthma.cellgeni.sanger.ac.uk, + covid19cellatlas.org +
A cellular census of human lungs identifies novel cell states in health and in asthma - bronchi + asthma.cellgeni.sanger.ac.uk, + covid19cellatlas.org +
Ischaemic sensitivity of human tissue by single cell RNA seq - lung + HCA, + covid19cellatlas.org +
Ischaemic sensitivity of human tissue by single cell RNA seq - spleen + HCA, + covid19cellatlas.org +
Ischaemic sensitivity of human tissue by single cell RNA seq - oesophagus + HCA, + covid19cellatlas.org +
Spatio-temporal immune zonation of the human kidney + www.kidneycellatlas.org, + covid19cellatlas.org +
Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics - 10x + E-MTAB-6701, + covid19cellatlas.org +
Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics - SmartSeq2 + E-MTAB-6701, + covid19cellatlas.org +
Gut Cell Atlas + www.gutcellatlas.org, + covid19cellatlas.org +
A single-cell atlas of the peripheral immune response to severe COVID-19 + Blish Lab, + medRxiv preprint +
Atlas of Healthy and SHIV-Infected Non-Human Primate Lung and Ileum ACE2+ Cells - Ileum + Single Cell Portal +
Atlas of Healthy and SHIV-Infected Non-Human Primate Lung and Ileum ACE2+ Cells - Lung + Single Cell Portal +
Allergic inflammatory memory in human respiratory epithelial progenitor cells - epithelial cells + Single Cell Portal +
Allergic inflammatory memory in human respiratory epithelial progenitor cells - nasal scrapings + Single Cell Portal +
Allergic inflammatory memory in human respiratory epithelial progenitor cells - surgical + Single Cell Portal +
Allergic inflammatory memory in human respiratory epithelial progenitor cells - nasal SSS + Single Cell Portal +
ACE2 and TMPRSS2 expression in human non-inflamed terminal ileum - epithelial cells + Single Cell Portal +
ACE2 and TMPRSS2 expression in human non-inflamed terminal ileum + Single Cell Portal +
Human Lung HIV-TB Co-infection ACE2+ Cells + Single Cell Portal +
Epithelial Cells in NHP mTB Granuloma and Uninvolved Lung + Single Cell Portal +
Selective Neuronal Vulnerability in Alzheimer's Disease + Kampmann Lab, + BioRxiv preprint +
Selective Neuronal Vulnerability in Alzheimer's Disease: Superior Frontal Gyrus + Kampmann Lab, + BioRxiv preprint +
Selective Neuronal Vulnerability in Alzheimer's Disease: Astrocytes in EC + Kampmann Lab, + BioRxiv preprint +
Selective Neuronal Vulnerability in Alzheimer's Disease: Excitatory Neurons in EC + Kampmann Lab, + BioRxiv preprint +
Selective Neuronal Vulnerability in Alzheimer's Disease: Inhibitory Neurons in EC + Kampmann Lab, + BioRxiv preprint +
Selective Neuronal Vulnerability in Alzheimer's Disease: Microglia in EC + Kampmann Lab, + BioRxiv preprint +
Selective Neuronal Vulnerability in Alzheimer's Disease: Astrocytes in SFG + Kampmann Lab, + BioRxiv preprint +
Selective Neuronal Vulnerability in Alzheimer's Disease: Excitatory Neurons in SFG + Kampmann Lab, + BioRxiv preprint +
Selective Neuronal Vulnerability in Alzheimer's Disease: Inhibitory Neurons in SFG + Kampmann Lab, + BioRxiv preprint +
Selective Neuronal Vulnerability in Alzheimer's Disease: Microglia in SFG + Kampmann Lab, + BioRxiv preprint +
Single-cell gene expression profiling of SARS-CoV-2 infected human cell lines - H1299 + Landthaler Lab, + BioRxiv preprint +
Single-cell gene expression profiling of SARS-CoV-2 infected human cell lines - Calu-3 + Landthaler Lab, + BioRxiv preprint +
Single-cell drug screening - A549 + Trapnell Lab Github, + Science +
Single-cell drug screening - K562 + Trapnell Lab Github, + Science +
Single-cell drug screening - MCF7 + Trapnell Lab Github, + Science +
A molecular atlas of cell types and zonation in the brain vasculature + Betsholtz Lab, + Nature +
Single Soma Transcriptomics - AT8 + bioRxiv preprint +
Single Soma Transcriptomics - MAP2 + bioRxiv preprint +
Single Soma Transcriptomics - MAP2AT8 + bioRxiv preprint +
Single-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cells + bioRxiv preprint +
+ +
+ +
+ + + + diff --git a/docs/_site/index.html b/docs/_site/index.html index 49e763a0..4d484f9b 100644 --- a/docs/_site/index.html +++ b/docs/_site/index.html @@ -7,7 +7,7 @@ Index | cellxgene - + @@ -16,10 +16,10 @@ +{"@type":"WebSite","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"headline":"Index","description":"An interactive explorer for single-cell transcriptomics data","url":"https://chanzuckerberg.github.io/cellxgene/","name":"cellxgene","@context":"https://schema.org"} - + @@ -86,6 +86,10 @@ + Extensions
+ + + Contact & finding help
diff --git a/docs/_site/posts/extensions.html b/docs/_site/posts/extensions.html new file mode 100644 index 00000000..5e38712b --- /dev/null +++ b/docs/_site/posts/extensions.html @@ -0,0 +1,152 @@ + + + + + + + + +Extensions | cellxgene + + + + + + + + + + + + + + + +
+
+ cellxgene + +

An interactive explorer for single-cell transcriptomics data

+

+ + + Quick start
+ + + + + Installation
+ + + + Gallery
+ + + + Demo datasets
+ + + + All other datasets
+ + + + Preparing your data
+ + + + Launching cellxgene
+ + + + Hosting cellxgene
+ + + + Annotating data
+ + + + Methods
+ + + + Troubleshooting
+ + + + Roadmap
+ + + + Contributing (ideas or code)
+ + + + Extensions
+ + + + Contact & finding help
+ + + + Code +

+
+ +
+

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.

+ +

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 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 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 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 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

+ +

Single Cell Portal

+ +

The Single Cell Portal is a data hosting and visualization service. cellxgene can be embedded as an additional view to complement the visualizations provided by the. +Example.

+ +

FASTGenomics

+ +

FASTGenomics 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 for data from Schulte-Schrepping et al. (Cell, 2020). +Note that it is not necessary to create an account, anonymous login is permitted.

+ +
+ +
+ + + + diff --git a/docs/_site/posts/extensions.md b/docs/_site/posts/extensions.md new file mode 100644 index 00000000..5b25c958 --- /dev/null +++ b/docs/_site/posts/extensions.md @@ -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. diff --git a/docs/posts/extensions.md b/docs/posts/extensions.md new file mode 100644 index 00000000..5b25c958 --- /dev/null +++ b/docs/posts/extensions.md @@ -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.