Databases with access to published single cell datasets for exploration and/or download

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)
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

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
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.
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
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