Resources
The following single-cell resources provide curated single-cell data in accordance with FAIR principles:
CELLxGENE
CELLxGENE is a suite of tools that help scientists to find, download, explore, analyze, annotate, and publish single-cell datasets. It includes several powerful tools with various features to help you engage with single-cell data.
Bgee
Bgee is a database for retrieval and comparison of gene expression patterns across multiple animal species, produced from multiple data types including bulk RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data. Bgee is based exclusively on curated wild-type expression data to provide a comparable reference of gene expression. Bgee produces calls of presence/absence of expression, and of differential over-/under-expression, integrated along with information on gene orthology, and homology between organs. This allows comparisons of expression patterns between species.
ASAP
ASAP (Automated Single-cell Analysis Portal) is an innovative collaborative platform designed for the comprehensive analysis of single-cell transcriptomics data. This user-friendly portal brings together researchers and bioinformaticians, providing a centralized space to delve into single-cell gene expression profiles. ASAP empowers users with the complete single-cell analysis pipeline, running fully online with step-by-step parametrization and interactive visualization of results. Additionally, ASAP features crowd-annotation, fostering collaboration between researchers and tissue experts. It has already been utilized to annotate ~500k cells in the Fly Cell Atlas, promoting better reproducibility, as the entire pipeline run on ASAP is executed within a downloadable Docker container.
Single Cell Portal
The Broad Institute's Single Cell Portal is an open-access platform designed to share, visualize, and explore single-cell omics data, including scRNA-seq, snRNA-seq, scATAC-seq, and multi-omics datasets. It provides interactive tools for navigating UMAP/t-SNE plots, examining gene expression across annotated cell types, and filtering or comparing datasets. Users can publish studies, download raw or processed data compatible with Seurat and Scanpy, and integrate with cloud-based pipelines (e.g., Terra on GCP). The portal supports rapid exploratory analysis and promotes reproducibility and open science in the single-cell community.
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