DVEXDrosophila Virtual Expression eXplorer
FASTGenomicsPlatform for single cell transcriptomics
LungAgingAtlasAn atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics
SPACEGERMSpatial Caenorhabditis elegans germline expression of mRNA & miRNA
stochprofMLWebtool to infer single-cell regulatory states from expression measurements taken from small groups of cells (averaging-and-deconvolution approach)
SVZ Cell AtlasMolecular cell atlas of the largest germinal region of the adult mouse brain, the subventricular zone (SVZ)
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)
ASAPAutomated Singel-cell Analysis Pipeline, web-based platform for the analysis and interactive visualization of single-cell RNA-seq data
Cancer SEACancer single cell state atlas, database that aims to comprehensively decode distinct functional states of cancer cells at single-cell resolution
Cell Atlas SearchHuman single cell RNA-seq Search Engine
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
CerebroCell report browser, which allows users to interactively visualize various parts of single cell transcriptomics data
conquerConsistent quantification of external rna-seq data, repository providing access to consistently processed public single-cell RNA-seq data sets
D3EDiscrete Distributional Differential Expression (D3E), tool for identifying differentially-expressed genes, based on single-cell RNA-seq data
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
HCA bone marrow viewerHuman Cell Atlas bone marrow single-cell interactive web portal
HCA Data PortalHuman Cell Atlas data portal
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 SummarizedExperiment Explorer, interactive user interface for exploring data in objects derived from the SummarizedExperiment class with particular focus on single-cell data stored in the SingleCellExperiment derived class
Jingle BellsRepository of standardized single cell RNA-aeq datasets for analysis and visualization at the single cell level
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)
PangloaDBDatabase for exploration of single cell RNA sequencing experiments from mouse and human
PIVOTPlatform for Interactive analysis and Visualization Of Transcriptomics data
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
SCPortalenSingle-cell centric database (human and mouse, transcriptomic and imaging)
scQueryWeb application for the comparitive analysis of single-cell RNA-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
SeuratV3WizardWeb-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat v3
SeuratWizardWeb-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat
Single Cell Expression AtlasSingle cell gene expression across species (EMBL-EBI)
Single Cell PortalSharing of scientific results and disseminating data generated from single cell technologies (Broad Institute)
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, or through a set of R functions through the command line
STREAMInteractive computational pipeline for reconstructing complex celluar developmental trajectories from sc-qPCR, scRNA-seq or scATAC-seq data
UCSC Cell BrowserViewer for single cell data
UCSC Xena single cell browserOnline exploration tool  for single cell RNA-seq data and associated meta-data and annotations