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celldepot

CellDepot: A unified repository for scRNA-seq data and visual exploration. J Mol Biol. 2021 Dec 28:167425. doi: 10.1016/j.jmb.2021.167425.

https://github.com/interactivereport/celldepot

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 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: biorxiv.org
  • ○
    Academic email domains
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    Institutional organization owner
  • ○
    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (13.2%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

CellDepot: A unified repository for scRNA-seq data and visual exploration. J Mol Biol. 2021 Dec 28:167425. doi: 10.1016/j.jmb.2021.167425.

Basic Info
  • Host: GitHub
  • Owner: interactivereport
  • Language: JavaScript
  • Default Branch: main
  • Homepage:
  • Size: 61.1 MB
Statistics
  • Stars: 24
  • Watchers: 6
  • Forks: 9
  • Open Issues: 2
  • Releases: 2
Created almost 5 years ago · Last pushed about 3 years ago
Metadata Files
Readme Citation

README.md

CellDepot: A unified repository for scRNAseq data and visual exploration

CellDepot containing over 270 datasets from 8 species and many tissues serves as an integrated web application to empower scientists in exploring single-cell RNA-seq (scRNA-seq) datasets and comparing the datasets among various studies through a user-friendly interface with advanced visualization and analytical capabilities. To begin with, it provides an efficient data management system that users can upload single cell datasets and query the database by multiple attributes such as species and cell types. In addition, the graphical multi-logic, multi-condition query builder and convenient filtering tool backed by MySQL database system, allows users to quickly find the datasets of interest and compare the expression of gene(s) across these. Moreover, by embedding the cellxgene VIP tool, CellDepot enables fast exploration of individual dataset in the manner of interactivity and scalability to gain more refined insights such as cell composition, gene expression profiles, and differentially expressed genes among cell types by leveraging more than 20 frequently applied plotting functions and high-level analysis methods in single cell research. In summary, the web portal available at http://celldepot.bxgenomics.com, prompts large scale single cell data sharing, facilitates meta-analysis and visualization, and encourages scientists to contribute to the single-cell community in a tractable and collaborative way. Finally, CellDepot is released as open-source software under MIT license to motivate crowd contribution, broad adoption, and local deployment for private datasets.

Cite: Lin D, Chen Y, Negi S, Cheng D, Ouyang Z, Sexton D, Li K, Zhang B. CellDepot: A unified repository for scRNA-seq data and visual exploration. J Mol Biol. 2021 Dec 28:167425. doi: 10.1016/j.jmb.2021.167425.

Public Web Portal

https://celldepot.bxgenomics.com

Pre-print

https://www.biorxiv.org/content/10.1101/2021.09.30.462602v1

CellDepot Tutorial

https://interactivereport.github.io/CellDepot/bookdown/docs/SITutorial.html

cellxgene VIP Tutorial

https://interactivereport.github.io/cellxgene_VIP/tutorial/docs/how-to-use-cellxgene-vip.html

CellDepot portal overview

Figure1

Data visualization and analysis by cellxgene VIP in CellDepot (Interactive Figure)

Figure2

Comparison matrix of scRNA-seq data portal tools

Table S1

Installation Guide

https://celldepot.bxgenomics.com/celldepot_manual

Owner

  • Name: Baohong Zhang
  • Login: interactivereport
  • Kind: user

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this package, please cite it as below."
preferred-citation:
  type: article
  authors:
  - family-names: "Lin"
    given-names: "Dongdong"
  - family-names: "Chen"
    given-names: "Yirui"
  - family-names: "Negi"
    given-names: "Soumya"
  - family-names: "Cheng"
    given-names: "Derrick"
  - family-names: "Zhengyu"
    given-names: "Ouyang"
  - family-names: "Sexton"
    given-names: "David"
  - family-names: "Li"
    given-names: "Kejie"
  - family-names: "Zhang"
    given-names: "Baohong"
  title: "CellDepot: A unified repository for scRNA-seq data and visual exploration"
  doi: "10.1016/j.jmb.2021.167425"
  journal: "J Mol Biol."
  year: 2021
  url: "https://www.sciencedirect.com/science/article/pii/S0022283621006665?via%3Dihub"

GitHub Events

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Dependencies

webapp/app/core/template/js/jsTree/3.10/bower.json bower
  • jquery >=1.9.1
webapp/app/core/template/js/jsTree/3.10/package.json npm
  • dox ~0.9.0 development
  • grunt ~1.0.0 development
  • grunt-contrib-concat * development
  • grunt-contrib-copy * development
  • grunt-contrib-imagemin ~2.0.1 development
  • grunt-contrib-jshint * development
  • grunt-contrib-less ~1.4.1 development
  • grunt-contrib-qunit ~2.0.0 development
  • grunt-contrib-uglify * development
  • grunt-contrib-watch ~1.1.0 development
  • grunt-resemble-cli 0.0.8 development
  • grunt-text-replace ~0.4.0 development
  • lodash ^4.17.10 development
  • jquery >=1.9.1
webapp/app/core/template/js/slimScroll/1.3.8/package.json npm
  • jquery >= 1.7
webapp/bxaf_lite/library/jquery-ui/package.json npm
  • commitplease 2.3.0 development
  • grunt 0.4.5 development
  • grunt-bowercopy 1.2.4 development
  • grunt-cli 0.1.13 development
  • grunt-compare-size 0.4.0 development
  • grunt-contrib-concat 0.5.1 development
  • grunt-contrib-csslint 0.5.0 development
  • grunt-contrib-jshint 0.12.0 development
  • grunt-contrib-qunit 1.0.1 development
  • grunt-contrib-requirejs 0.4.4 development
  • grunt-contrib-uglify 0.11.1 development
  • grunt-git-authors 3.1.0 development
  • grunt-html 6.0.0 development
  • grunt-jscs 2.1.0 development
  • load-grunt-tasks 3.4.0 development
  • rimraf 2.5.1 development
  • testswarm 1.1.0 development
webapp/app/core/template/js/jsTree/3.10/composer.json packagist
  • components/jquery >=1.9.1
webapp/app/core/template/php/others/Simple_HTML_DOM_Parser/2.0R2/composer.json packagist
  • phpunit/phpunit ^6 || ^7 development
  • ext-iconv *
  • php >=5.6
webapp/bxaf_lite/library/phpmailer/composer.json packagist
  • phpdocumentor/phpdocumentor * development
  • phpunit/phpunit 4.7.* development
  • php >=5.0.0
webapp/bxaf_lite/library/phpmailer/composer.lock packagist
  • cilex/cilex 1.1.0 development
  • cilex/console-service-provider 1.0.0 development
  • container-interop/container-interop 1.1.0 development
  • doctrine/annotations v1.2.7 development
  • doctrine/instantiator 1.0.5 development
  • doctrine/lexer v1.0.1 development
  • erusev/parsedown 1.6.0 development
  • herrera-io/json 1.0.3 development
  • herrera-io/phar-update 1.0.3 development
  • jms/metadata 1.5.1 development
  • jms/parser-lib 1.0.0 development
  • jms/serializer 1.1.0 development
  • justinrainbow/json-schema 1.6.1 development
  • kherge/version 1.0.1 development
  • monolog/monolog 1.19.0 development
  • nikic/php-parser v1.4.1 development
  • phpcollection/phpcollection 0.4.0 development
  • phpdocumentor/fileset 1.0.0 development
  • phpdocumentor/graphviz 1.0.4 development
  • phpdocumentor/phpdocumentor v2.9.0 development
  • phpdocumentor/reflection 3.0.1 development
  • phpdocumentor/reflection-docblock 2.0.4 development
  • phpoption/phpoption 1.5.0 development
  • phpspec/prophecy v1.6.1 development
  • phpunit/php-code-coverage 2.2.4 development
  • phpunit/php-file-iterator 1.4.1 development
  • phpunit/php-text-template 1.2.1 development
  • phpunit/php-timer 1.0.8 development
  • phpunit/php-token-stream 1.4.8 development
  • phpunit/phpunit 4.7.7 development
  • phpunit/phpunit-mock-objects 2.3.8 development
  • pimple/pimple v1.1.1 development
  • psr/log 1.0.0 development
  • sebastian/comparator 1.2.0 development
  • sebastian/diff 1.4.1 development
  • sebastian/environment 1.3.7 development
  • sebastian/exporter 1.2.2 development
  • sebastian/global-state 1.1.1 development
  • sebastian/recursion-context 1.0.2 development
  • sebastian/version 1.0.6 development
  • seld/jsonlint 1.4.0 development
  • symfony/config v2.8.7 development
  • symfony/console v2.8.7 development
  • symfony/event-dispatcher v2.8.7 development
  • symfony/filesystem v3.0.7 development
  • symfony/finder v2.8.7 development
  • symfony/polyfill-mbstring v1.2.0 development
  • symfony/process v2.8.7 development
  • symfony/stopwatch v2.8.7 development
  • symfony/translation v3.0.7 development
  • symfony/validator v2.8.7 development
  • symfony/yaml v3.1.1 development
  • twig/twig v1.24.1 development
  • zendframework/zend-cache 2.7.1 development
  • zendframework/zend-config 2.6.0 development
  • zendframework/zend-eventmanager 3.0.1 development
  • zendframework/zend-filter 2.7.1 development
  • zendframework/zend-hydrator 1.1.0 development
  • zendframework/zend-i18n 2.7.3 development
  • zendframework/zend-json 3.0.0 development
  • zendframework/zend-serializer 2.8.0 development
  • zendframework/zend-servicemanager 2.7.6 development
  • zendframework/zend-stdlib 2.7.7 development
  • zetacomponents/base 1.9 development
  • zetacomponents/document 1.3.1 development
requirements.txt pypi
  • anndata >=0.7.4
  • cellxgene >=0.16
  • cellxgene_VIP >=2.0
  • diffxpy >=0.7.4
  • plotly >=4.8.1
  • scanpy >=1.5.0
  • seurat ==3.0.2
webapp/app/core/template/js/slimScroll/1.3.8/bower.json bower