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.
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