Databases

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

DVEX 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 Interactive exploration of human liver cell atlas (data from Aizarani et al. 2019)
LungAgingAtlas 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 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 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 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 datasets10x Genomics single cell gene expression datasets
Allen Brain AtlasBrain cell database containing electrophysiological, morphological, and transcriptomic data measured from individual cells (human and mouse)
Brain Immune AtlasResource 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 SEACancer single cell state atlas, database involving 14 functional states of 41,900 cancer single cells from 25 cancer types
conquerConsistent quantification of external RNA-seq data, repository providing access to consistently processed public single-cell RNA-seq data sets
Curated Database of single-cell studiesExhaustive, 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
DropVizExploring 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 viewerHuman 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 PortalHuman Cell Atlas data portal, community generated, multi-omic, open data processed by standardized pipelines
Jingle BellsRepository of standardized single cell RNA-seq datasets for analysis and visualization at the single cell level
LungGENSLung Gene Expression iN Single-cell, web-based tool for mapping single-cell gene expression in the developing lung
MOCAMouse Organogenesis Cell Atlas, single cell transcriptional landscape of mouse organogenesis (data from Cao et al. 2019)
Mouse Cell AtlasCollection of single-cell transcriptomic profiles from mouse tissues, organs, and cell cultures, web-based “single-cell MCA analysis” pipeline
Mouse sci-ATAC-seq AtlasAtlas 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 atlasDatabase 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)
PangloaDBDatabase for exploration of single cell RNA sequencing experiments from mouse and human
SCDevDBSingle-Cell Developmental Data Base, database to investigate single-cell gene expression profiling during different developmental pathways
SCPortalenSingle-cell centric database (human and mouse, transcriptomic and imaging)
scQueryWeb 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 datasetsCollection of publicly available datasets used by the Hemberg Group at the Sanger Institute
scRNASeqDBDatabase 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
SHOGoiNRepository for accumulating and integrating diverse human cell information to support a wide range of cell research at the single-cell resolution
Single Cell Expression AtlasSingle cell gene expression across species (EMBL-EBI), website including 151 single cell RNA-Seq studies from 14 species
Single Cell PortalSharing of scientific results and disseminating data generated from single cell technologies (Broad Institute)
Single-cell atlas of Alzheimer’s DiseaseSingle-cell atlas of the Entorhinal Cortex in Human Alzheimer’s Disease (data from Grubman et al. 2019)
Single-Cell RNA-seqSingle-cell RNA-seq data portal of DRSC/Perrimon lab (Drosophila datasets)
Single-cell RNA-seq data of mouse embryosSingle-cell RNA-seq data of E8.25 whole mouse embryos (data from Ibarra-Soria et al. 2018)
Tabula murisCompendium of single cell transcriptome data from the model organism Mus musculus, containing nearly 100,000 cells from 20 organs and tissues
UCSC Cell BrowserInteractive viewer for single cell data
UCSC Xena single cell browserOnline 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

FASTGenomicsOpen 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
stochprofMLWebtool to infer single-cell regulatory states from expression measurements taken from small groups of cells (averaging-and-deconvolution approach)
ASAPAutomated Singel-cell Analysis Pipeline, web-based platform for the analysis and interactive visualization of single-cell RNA-seq data
Cell Atlas SearchHuman 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 BLASTBLAST-like toolkit for scRNA-seq data querying and annotation
CellViewWeb application for exploratory data analysis of processed RNA-Seq data of single cell experiments
cellxgeneAn interactive explorer for single-cell transcriptomics data (app)
CerebroCell report browser, allows users to interactively visualize various parts of single cell transcriptomics data
ChromSCapeShiny/R application for interactive analysis of single-cell chromatin profiles from count matrices to differential analysis & gene set enrichment analysis
D3EDiscrete Distributional Differential Expression (D3E), tool for identifying differentially-expressed genes, based on single-cell RNA-seq data
Galaxy Single Cell Omics WorkbenchComprehensive set of analysis tools and consolidated workflows, comprising more than 20 bioinformatics tools dedicated to different research areas of single cell biology
GinkgoWeb tool for analyzing single-cell sequencing data (single-cell copy-number variation analysis)
GranatumGraphical single-cell RNA-seq (scRNA-seq) analysis pipeline for genomics scientists
is-CellRInteractive platform for Single-cell RNAseq (is-CellR), web-based Shiny application designed to provide a comprehensive analysis of single-cell RNA sequencing data
iSEEinteractive Summarized Experiment Explorer, interactive user interface for exploring data in objects derived from the SummarizedExperiment class with particular focus on single-cell data
Mouse Cell AtlasCollection of single-cell transcriptomic profiles from mouse tissues, organs, and cell cultures, web-based “single-cell MCA analysis” pipeline
NASQARNucleic Acid SeQuence Analysis Resource (NASQAR), web-based platform for high-throughput sequencing data analysis and visualization (e.g. single cell RNA-seq)
PIVOTPlatform for Interactive analysis and Visualization Of Transcriptomics data (based on the Shiny framework)
scClustVizInteractive R Shiny tool for visualizing single-cell RNAseq clustering results from common analysis pipelines
scOrangeInteractive data visualization and easy to use machine learning methods for single cell data
scQueryWeb 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
SCRATSingle-Cell Regulome Analysis Toolbox with a graphical user interface, for studying cell heterogeneity using single-cell regulome data (sc-ATAC, sc-DNAse, sc-ChIP)
SeuratV3WizardWeb-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat v3
SHoGoiN CELLBLASTSystem for searching gene expression databases for similar cells to the query gene expression profile
Single Cell Viewer (SCV)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
singleCellTKSingle 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
SPARWebserver for the interactive analyses and visualization of (single cell) small RNA sequencing data
SPRINGTool for uncovering high-dimensional structure in single-cell gene expression data
STREAMSingle-cell Trajectories Reconstruction, interactive computational pipeline for reconstructing complex celluar developmental trajectories from sc-qPCR, scRNA-seq or scATAC-seq data
V-SVAVisual Surrogate Variable Analysis, R Shiny application for detecting and annotating hidden sources of variation in single cell RNA-seq data