This repository is a comprehensive, community-curated list of single-cell RNA sequencing (scRNA-seq) analysis tools, papers, and resources. It aims to provide a structured overview of the rapidly evolving landscape of scRNA-seq analysis, serving researchers and bioinformaticians by cataloging methods for every stage of the analysis pipeline, from preprocessing to advanced downstream applications.

How It Works

The repository organizes a vast collection of tools and publications into logical categories, covering preprocessing, normalization, integration, dimensionality reduction, clustering, trajectory inference, differential expression, and various downstream analyses like cell-cell communication and spatial transcriptomics. Each entry typically includes a brief description, relevant papers, and links to software implementations, facilitating efficient discovery and evaluation of relevant methods.

Quick Start & Requirements

This is a curated list, not a software package. No installation is required. Users can navigate the extensive table of contents to find specific tools or topics of interest.

Highlighted Details

• Comprehensive coverage of scRNA-seq analysis steps, including specialized areas like RNA velocity, spatial transcriptomics, and multi-omics integration.
• Extensive cross-referencing with key publications, providing direct links to seminal papers and recent advancements.
• Includes resources for learning, such as tutorials, courses, and best practice guides, alongside databases and benchmark studies.
• Regularly updated to reflect the latest tools and methodologies in the field.

Maintenance & Community

The repository is maintained by mdozmorov and actively encourages community contributions and engagement. Links to related resources like scATAC-seq notes are provided.

Licensing & Compatibility

The repository itself is a collection of links and information, not software. The licensing of individual tools mentioned would need to be checked on their respective project pages.

Limitations & Caveats

As a curated list, the primary limitation is the potential for outdated information if not actively maintained. The sheer volume of tools means some may be missed, and the rapid pace of the field requires continuous updates.