FlyBase:ScRNA-Seq

Single Cell RNA-seq Data Portals

Resource	Description	Institution/Source
DRscDB	DRSC scRNA-seq DataBase (DRscDB) was built based on the information curated from Drosophila scRNA-seq publications and selected publications from other major model organisms (zebrafish, mouse and human) relevant to the tissue types that are common among the species chosen. Users can mine and compare the gene expression profiles at single-cell level across studies, tissues and species for any input gene. Users can also use DRscDB to analyze an input gene list, looking for marker genes enriched in tissues and cell types based in the same or other species. This makes it possible to compare different datasets across studies, tissues and species, and can facilitate cell type assignment for clusters identified from newly obtained scRNA-seq datasets.	DRSC, Harvard Medical School Boston, MA, USA
SCEA	Single Cell Expression Atlas (SCEA) is an open science bioinformatics resource that provides free access to gene expression data generated in experiments performed in different laboratories around the world at single cell resolution. The SCEA reprocesses raw scRNA-Seq data in a standardised way, in-house, and provides to the life sciences community uniform gene expression data across multiple species that are available both for download and for exploration via gene-oriented queries and visualisation online. The Atlas includes data from all popular single cell RNA-seq technologies, including SMART-like and Droplet. Fly datasets in SCEA can be accessed directly at [1]	SCEA EMBL-EBI, Wellcome Genome Campus Hinxton, UK

Single Cell RNA-seq Data Analysis Tools

Resource	Description	Source/Reference
ASAP	The web-based, collaborative portal ASAP (Automated Single-cell Analysis Portal) was developed with as primary goal to democratize complex single-cell omics data analyses (scRNA-seq and more recently scATAC-seq). By taking advantage of a Docker system to enhance reproducibility, and novel bioinformatics approaches that were recently developed for improving scalability, ASAP meets challenging requirements set by recent cell atlasing efforts such as the Human (HCA) and Fly (FCA) Cell Atlas Projects. Specifically, ASAP can now handle datasets containing millions of cells, integrating intuitive tools that allow researchers to collaborate on the same project synchronously. ASAP tools are versioned, and researchers can create unique access IDs for storing complete analyses that can be reproduced or completed by others. Finally, ASAP does not require any installation and provides a full and modular single-cell RNA-seq analysis pipeline.	EPFL Swiss Institute of Bioinformatics Lausanne, Switzerland
cisTopic	cisTopic is an R package to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.	VIB Center for Brain & Disease Research Department of Human Genetics, KU Leuven Leuven, Belgium
SCENIC R Package SCENIC Python package	SCENIC infers Gene Regulatory Networks and cell types from single-cell RNA-seq data.	Center for Brain & Disease Research KU Leuven VIB Center for Cancer Biology Leuven, Belgium University of Liege Liege, Belgium https://europepmc.org/article/MED/28991892 https://europepmc.org/article/MED/32561888
SCope	SCope is a fast visualization tool for large-scale and high dimensional scRNA-seq and scATAC-seq datasets.	VIB KU Leuven Leuven, Belgium https://europepmc.org/article/PPR/PPR21077
VSN	VSN-Pipelines is a repository of pipelines for single-cell data analysis in Nextflow DSL2. It contains multiple workflows for analyzing single cell transcriptomics data, and was used for the automated analysis of the Fly Cell Atlas.