Databases
Databases with access to published single cell datasets for exploration and/or download
Databases from SCOG partners
DVEX | Ref | Drosophila Virtual Expression eXplorer, online resource tool which offers an easy way to explore the transcriptome of the stage 6 Drosophila embryo at the single cell level (data from Karaiskos et al. 2017) |
Human Liver Cell Atlas | Ref | Interactive exploration of human liver cell atlas (data from Aizarani et al. 2019) |
LungAgingAtlas | Ref | Interactive user-friendly webtool to access the atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics (data from Angelidis et al. 2019) |
ShinyCortex | Ref | Resource that brings together data from recent scRNA-seq studies of the developing cortex for further analysis, displaying recently published scRNA-seq data from the human and mouse cortex in a comprehensible, dynamic and accessible way, suitable for data exploration by biologists |
SPACEGERM | Ref | Spatial Caenorhabditis elegans germline expression of mRNA & miRNA, interactive data visualization tool for exploring the spatiotemporal expression data in the germline (data from Diag et al. 2018) |
SVZ Cell Atlas | Ref | Interactive online tool to access and visualize molecular cell atlas of the largest germinal region of the adult mouse brain, the subventricular zone (SVZ) (data from Zywitza et al. 2018) |
Further Databases
10x Genomics datasets | 10x Genomics single cell gene expression datasets | |
Allen Brain Atlas | Brain cell database containing electrophysiological, morphological, and transcriptomic data measured from individual cells (human and mouse) | |
Brain Immune Atlas | Ref | Resource and visualization tool for assessing various single-cell RNA sequencing datasets that together capture the diversity of the brain immune compartment (data from Van Hove et al. 2019) |
Cancer SEA | Ref | Cancer single cell state atlas, database involving 14 functional states of 41,900 cancer single cells from 25 cancer types |
conquer | Ref | Consistent quantification of external RNA-seq data, repository providing access to consistently processed public single-cell RNA-seq data sets |
Curated Database of single-cell studies | Ref | Exhaustive, manually curated database of single-cell transcriptomics studies with key information: descriptions of the type of data and technologies used, along with descriptors of the biological systems studied |
DropViz | Ref | Exploring the Mouse Brain through Single Cell Expression Profiles, adult mouse brain cell atlas (690,000 individual cells from nine different regions) accessible through interactive online software |
HCA bone marrow viewer | Ref | Human Cell Atlas bone marrow single-cell interactive web portal, provides navigable results from the first large-scale release from the HCA bone marrow tissue project |
HCA Data Portal | Human Cell Atlas data portal, community generated, multi-omic, open data processed by standardized pipelines | |
HuBMAP Data Portal | Central resource for discovery, visualization, and download of single-cell tissue data generated by the Human BioMolecular Atlas Program consortium. A standardized data curation and processing workflow ensure that only high quality is released. | |
Jingle Bells | Ref | Repository of standardized single cell RNA-seq datasets for analysis and visualization at the single cell level |
LungGENS | Ref | Lung Gene Expression iN Single-cell, web-based tool for mapping single-cell gene expression in the developing lung |
MOCA | Ref | Mouse Organogenesis Cell Atlas, single cell transcriptional landscape of mouse organogenesis (data from Cao et al. 2019) |
Mouse Cell Atlas | Ref | Collection of single-cell transcriptomic profiles from mouse tissues, organs, and cell cultures, web-based “single-cell MCA analysis” pipeline |
Mouse sci-ATAC-seq Atlas | Ref | Atlas of chromatin accessibility in mouse at single cell resolution, 17 samples spanning 13 different tissues in 8-week old mice (data from Cusanovich et al. 2018) |
Murine aging cell atlas | Ref | Database of RNA-seq data for >50,000 cells from kidney, lung, and spleen in young (7 months) and aged (22-23 months) mice (data from Kimmel et al. 2019) |
PangloaDB | Ref | Database for exploration of single cell RNA sequencing experiments from mouse and human |
SCDevDB | Ref | Single-Cell Developmental Data Base, database to investigate single-cell gene expression profiling during different developmental pathways |
SCPortalen | Ref | Single-cell centric database (human and mouse, transcriptomic and imaging) |
scQuery | Ref | Web server for the comparitive analysis of single-cell RNA-seq data, utilizing scRNA-seq data collected from over 500 different experiments for the analysis of new scRNA-Seq data |
scRNA-seq datasets | Collection of publicly available datasets used by the Hemberg Group at the Sanger Institute | |
scRNASeqDB | Ref | Database for gene expression profiling in human single cell by RNA-seq, containing 36 human single cell gene expression data sets involving 8910 cells from 174 cell groups |
SHOGoiN | Repository for accumulating and integrating diverse human cell information to support a wide range of cell research at the single-cell resolution | |
Single Cell Expression Atlas | Ref | Single cell gene expression across species (EMBL-EBI), website including 151 single cell RNA-Seq studies from 14 species |
Single Cell Portal | Sharing of scientific results and disseminating data generated from single cell technologies (Broad Institute) | |
Single-cell atlas of Alzheimer’s Disease | Ref | Single-cell atlas of the Entorhinal Cortex in Human Alzheimer’s Disease (data from Grubman et al. 2019) |
Single-Cell RNA-seq | Single-cell RNA-seq data portal of DRSC/Perrimon lab (Drosophila datasets) | |
Single-cell RNA-seq data of mouse embryos | Ref | Single-cell RNA-seq data of E8.25 whole mouse embryos (data from Ibarra-Soria et al. 2018) |
Tabula muris | Ref | Compendium of single cell transcriptome data from the model organism Mus musculus, containing nearly 100,000 cells from 20 organs and tissues |
UCSC Cell Browser | Interactive viewer for single cell data | |
UCSC Xena single cell browser | Online exploration tool for single cell RNA-seq data and associated meta-data and annotations |
Web portals and apps
Web portals and (Shiny) apps for interactive analysis and/or visualization of your single cell data
Web portal and apps from SCOG partners
FASTGenomics | Ref | Open online platform for single-cell RNA-seq, provides state-of-the-art data management and analytics and enables collaborators to share large data sets and use cutting-edge AI-based analysis methods with high demand on computational power |
Galaxy HiCExplorer 3 | Ref | Web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization |
Galaxy Single Cell Omics Workbench | Comprehensive set of analysis tools and consolidated workflows, comprising more than 20 bioinformatics tools dedicated to different research areas of single cell biology | |
scbrowse | Interactive browser for single-cell ATAC-seq data, allowing to simultaneously explore the accessibility patterns of selected cells in the embedding space and for selected genomic regions | |
stochprofML | Webtool to infer single-cell regulatory states from expression measurements taken from small groups of cells (averaging-and-deconvolution approach) | |
SCelVis | Ref | Easy Single-Cell Visualization, exploratory single cell data analysis on the desktop and in the cloud |
Further Web portals and apps
ASAP | Ref | Automated Singel-cell Analysis Pipeline, web-based platform for the analysis and interactive visualization of single-cell RNA-seq data |
Bbrowse | Platform for single cell transcriptome analysis and spatial transcriptomics, access to published datasets and analysis of own data (free academic users can access up to 5 public studies in the database, import Seurat or Scanpy objects, and run almost all downstream analyses in the software). | |
Cell Atlas Search | Ref | Human single cell RNA-seq Search Engine, query with single-cell expression profiles to retrieve top matches from a large database of the sc and bulk expression profiles with meta-information |
Cell BLAST | Ref | BLAST-like toolkit for scRNA-seq data querying and annotation |
CellView | Ref | Web application for exploratory data analysis of processed RNA-Seq data of single cell experiments |
cellxgene | An interactive explorer for single-cell transcriptomics data (app) | |
Cerebro | Ref | Cell report browser, allows users to interactively visualize various parts of single cell transcriptomics data |
Cirrocumulus | Interactive visualization tool for large-scale single-cell genomics data | |
CReSCENT | Ref | CanceR Single Cell ExpressioN Toolkit, intuitive and scalable web portal incorporating a containerized pipeline execution engine for standardized analysis of single-cell RNA sequencing data, populated with public datasets and preconfigured pipelines |
ChromSCape | Ref | Shiny/R application for interactive analysis of single-cell chromatin profiles from count matrices to differential analysis & gene set enrichment analysis |
D3E | Ref | Discrete Distributional Differential Expression (D3E), tool for identifying differentially-expressed genes, based on single-cell RNA-seq data |
Ginkgo | Ref | Web tool for analyzing single-cell sequencing data (single-cell copy-number variation analysis) |
Granatum | Ref | Graphical single-cell RNA-seq (scRNA-seq) analysis pipeline for genomics scientists |
GranatumX | Ref | Community engaging, modularized and flexible software environment for single-cell analysis, webtool for processing, analysis and visualization of scRNA-Seq data. |
histoCAT | Ref | Histology Topography Cytometry Analysis Toolbox, interactive, quantitative, and comprehensive exploration of multiplexed image cytometry data. |
IRIS3 | Ref | Integrated Cell-type-specific Regulon Inference Server from Single-cell RNA-Seq, integrated web server for cell-type-specific regulon (CTSR) prediction from Human or Mouse Single-cell RNA-Seq data |
is-CellR | Ref | Interactive platform for Single-cell RNAseq (is-CellR), web-based Shiny application designed to provide a comprehensive analysis of single-cell RNA sequencing data |
iSEE | Ref | interactive Summarized Experiment Explorer, interactive user interface for exploring data in objects derived from the SummarizedExperiment class with particular focus on single-cell data |
Loom Viewer | Tool for sharing, browsing and visualizing single-cell data stored in the Loom file format. | |
Loupe Browser | Visualization software that provides intuitive analysis functionality to explore 10x Genomics data, easy-to-use desktop application. | |
Methylscaper | Ref | R/shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data |
Millefy | Ref | Tool for visualizing read coverage of scRNA-seq datasets in genomic context, dynamically and automatically reordering single cells based on ‘locus-specific’ pseudotime and highlighting cell-to-cell heterogeneity in read covreage of scRNA-seq data |
Mouse Cell Atlas | Ref | Collection of single-cell transcriptomic profiles from mouse tissues, organs, and cell cultures, web-based “single-cell MCA analysis” pipeline |
NASQAR | Ref | Nucleic Acid SeQuence Analysis Resource (NASQAR), web-based platform for high-throughput sequencing data analysis and visualization (e.g. single cell RNA-seq) |
PIVOT | Ref | Platform for Interactive analysis and Visualization Of Transcriptomics data (based on the Shiny framework) |
scClustViz | Ref | Interactive R Shiny tool for visualizing single-cell RNAseq clustering results from common analysis pipelines |
scfind | Ref | Single-cell analysis tool that facilitates fast search of biologically or clinically relevant marker genes in cell atlases, interactive interface website with 9 single cell datasets (code for scfind is available at github). |
SCHNAPPs | Ref | Single Cell sHiNy APPlication(s), Shiny-based application designed to enable bench-scientists to autonomously explore and interpret single cell RNA-seq expression data and associated annotations. |
SCope | Ref | Fast visualization tool for large-scale and high dimensional single-cell data, webtool to test out SCope on several published or own uploaded datasets (visit github to run SCope via standalone app or command line) |
scOrange | Ref | Interactive data visualization and easy to use machine learning methods for single cell data |
scQuery | Ref | Web server for the comparitive analysis of single-cell RNA-seq data, utilizing scRNA-seq data collected from over 500 different experiments for the analysis of new scRNA-Seq data |
SCRAT | Ref | Single-Cell Regulome Analysis Toolbox with a graphical user interface, for studying cell heterogeneity using single-cell regulome data (sc-ATAC, sc-DNAse, sc-ChIP) |
scSVA | Ref | Single-cell Scalable Visualization and Analytics, interactive visualization and exploratory analysis of massive single-cell omics datasets. |
SeuratV3Wizard | Web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat v3 | |
SHoGoiN CELLBLAST | System for searching gene expression databases for similar cells to the query gene expression profile | |
Single Cell Explorer | Ref | Freely-available single cell transcriptomic analysis tool that enables computational and experimental biologists to collaboratively explore, annotate, and share results in a flexible software environment and a centralized database server that supports data portal functionality. |
Single Cell Viewer (SCV) | Ref | Shiny application that offers rich visualization, advanced data filtering/segregation, and on-the-fly differential gene analysis for single-cell datasets using minimally-curated Seurat v3 objects as input |
singleCellTK | Ref | Single Cell Toolkit, interactive scRNA-Seq analysis package that allows users to upload raw scRNA-Seq count matrices and perform downstream scRNA-Seq analysis interactively through a web interface |
SPAR | Ref | Webserver for the interactive analyses and visualization of (single cell) small RNA sequencing data |
SPOT | Ref | Web-tool enabling swift profiling of transcriptomes |
SPRING | Ref | Tool for uncovering high-dimensional structure in single-cell gene expression data |
STREAM | Ref | Single-cell Trajectories Reconstruction, interactive computational pipeline for reconstructing complex celluar developmental trajectories from sc-qPCR, scRNA-seq or scATAC-seq data |
UNCURL | Ref | Online GUI-based interactive scRNA-Seq analysis tool, combining data preprocessing, dimensionality reduction, clustering, differential expression, and interactive data analysis within an online graphical user interface. |
Vitessce | Visual integration tool for exploration of spatial single cell experiments, modular design optimized for scalable, linked visualizations that support the spatial and non-spatial representation of tissue-, cell- and molecule-level data. | |
V-SVA | Ref | Visual Surrogate Variable Analysis, R Shiny application for detecting and annotating hidden sources of variation in single cell RNA-seq data |