awesome-single-cell
github.com/seandavi/awesome-single-cell ↗Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
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Installation instructions →What's inside
Web portals, apps, and databases
- 10X Genomics datasetsWeb portals and databases
10x genomics public datasets, including 1.3M cell mouse brain dataset.
- ASAPWeb portals and databases
Automated Single-cell Analysis Pipeline (deposited in
- Asc-SeuratInteractive visualization and analysis
[R, Docker] - Asc-Seurat is a web application based on
- CellarInteractive visualization and analysis
[Python] - Cellar is an easy to use, interactive, and comprehensive software tool for the assignment of cell types in single-cell studies. It supports preprocessing, dimensionality reduction, clustering, differential expression & enrichment analysis, spatial transcriptomics, label transfer, semi-supervised clustering and more. A live web server running Cellar is available
- Cell_BLASTWeb portals and databases
A Web portal powered by Cell_BLAST (scRNA-seq querying tool) and ACA (scRNA-seq database).
- cellBrowserInteractive visualization and analysis
[Python, Javascript] Python pipeline and Javascript scatter plot library for single-cell datasets.
People
- Aaron Lun (Cancer Research UK, UK)Male
- Ahmet Coskun (Georgia Tech, USA)Male
- Alicia Oshlack (Murdoch Children's Research Institute, Australia)Female
- Aviv Regev (Broad Institute, USA)Female
- Barbara Di Camillo (Information Engineering Department, University of Padova, ItalyFemale
- Barbara Treutlein (ETH Zurich, CH)Female
Tutorials and workflows
- Aaron Lun's Single Cell workflow on Bioconductor
[R] - This article describes a computational workflow for basic analysis of scRNA-seq data using software packages from the open-source Bioconductor project.
- Analysis of single cell RNA-seq data
[R and Python] - The
- ATAC-Seq Pipeline
[Shell and R] -
- Bioconductor2016 Single-cell-RNA-sequencing workshop by Sandrine Dudoit lab
[R] - SCONE, clusterExperiment, and slingshot tutorial.
- Clustering 3K PBMCs with Scanpy in Galaxy
Galaxy Training Material.
- CRUK CI Introduction to single-cell RNA-seq data analysis
website
Journal articles of general interest
- A comparison of single-cell trajectory inference methodsMethods comparisons
Unsure which of the more than 70
- Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic dataMethods comparisons
a comparison of gene regulatory network inference methods using simulated and real single-cell RNA-seq datasets
- Bias, Robustness And Scalability In Differential Expression Analysis Of Single-Cell RNA-Seq DataMethods comparisons
comparison of 36 statistical methods to detect differentially expressed genes between two annotated populations from the
- BioMedCentral Single-Cell -omics collectionPaper collections
- Comparative analysis of single-cell RNA sequencing methodsMethods comparisons
a comparison of wet lab protocols for scRNA sequencing.
- Comparison of computational methods for imputing single-cell RNA-sequencing dataMethods comparisons
We compared eight imputation methods, evaluated their power in recovering original real data, and performed broad analyses to explore their effects on clustering cell types, detecting differentially expressed genes, and reconstructing lineage trajectories in the context of both simulated and real data. Simulated datasets and case studies highlight that there are no one method performs the best in all the situations.
Similar lists and collections
- agitter's Pseudotime estimation list
An overview of algorithms for estimating pseudotime in single-cell RNA-seq data.
- CrazyHotTommy's RNA-seq analysis list
Very broad list that includes some single cell RNA-seq packages and papers.
Software packages
- alevin-fryRNA-seq
[Rust] - 🐟 Rapid, accurate and memory-frugal preprocessing of single-cell and single-nucleus RNA-seq data.
- AMULETDoublet Identification
[shell, Python, R] - A count based method for detecting multiplets from single nucleus ATAC-seq (snATAC-seq) data.
- anchorRNA-seq
[Python] - ⚓ Find bimodal, unimodal, and multimodal features in your data
- aneufinderCopy number analysis
[R] - Bioconductor module for copy-number detection in single-cell whole genome sequencing (scWGS) and strand-seq data using a Hidden Markov Model or binary bisection method.
- AnnSQLRNA-seq
[Python] - ⛃ The AnnSQL package enables SQL based queries on AnnData objects using the DuckDB in-process database engine.
- APackOfTheClonesImmune receptor profiling
[R] -
Showing a sample of 505 resources. View the full list on GitHub →