Table of software for the analysis of single-cell RNA-seq data.
☆341Mar 20, 2026Updated this week
Alternatives and similar repositories for scRNA-tools
Users that are interested in scRNA-tools are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- R package for analyzing single-cell RNA-seq data☆179Feb 29, 2024Updated 2 years ago
- Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.☆3,678Mar 9, 2026Updated 2 weeks ago
- An overview of algorithms for estimating pseudotime in single-cell RNA-seq data☆438Updated this week
- Simple simulation of single-cell RNA sequencing data☆233Jan 12, 2026Updated 2 months ago
- scRNAseq analysis notes from Ming Tang☆789Dec 2, 2024Updated last year
- A list of scRNA-seq analysis tools☆780Mar 9, 2026Updated 2 weeks ago
- R package for integrating and analyzing multiple single-cell datasets☆427Feb 4, 2026Updated last month
- Interactively analyze single cell genomic data☆186Jan 14, 2026Updated 2 months ago
- Multi-sample multi-group scRNA-seq analysis tools☆221Mar 8, 2026Updated 2 weeks ago
- Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).☆88Dec 4, 2025Updated 3 months ago
- Tools and methods for analysis of single cell assay data in R☆262Oct 17, 2025Updated 5 months ago
- Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data☆238May 8, 2023Updated 2 years ago
- Code and analysis for the 1000 tools paper☆11Nov 12, 2021Updated 4 years ago
- Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially ex…☆107Aug 1, 2023Updated 2 years ago
- Doublet detection in single-cell RNA-seq data.☆97Feb 6, 2025Updated last year
- Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq an…☆1,559Dec 11, 2022Updated 3 years ago
- Analysis of single cell RNA-seq data course☆679Apr 11, 2022Updated 3 years ago
- Reference mapping for single-cell genomics☆400Dec 2, 2025Updated 3 months ago
- Fast, sensitive and accurate integration of single-cell data with Harmony☆625Oct 10, 2025Updated 5 months ago
- Content for the OSCA Book.☆66Mar 15, 2023Updated 3 years ago
- This contains the dataset for comparing scRNA-seq analysis methods☆93Aug 26, 2020Updated 5 years ago
- SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.☆479Apr 5, 2024Updated last year
- R toolkit for single cell genomics☆2,689Updated this week
- MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological …☆379Oct 3, 2024Updated last year
- Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕☆185Jun 24, 2021Updated 4 years ago
- An interactive explorer for single-cell transcriptomics data☆756Updated this week
- Normalization for single cell RNA-seq data☆51Jun 11, 2025Updated 9 months ago
- Clone of the Bioconductor repository for the scater package.☆95Jan 12, 2026Updated 2 months ago
- Single-cell analysis in Python. Scales to >100M cells.☆2,379Updated this week
- R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets☆246Mar 8, 2026Updated 2 weeks ago
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆317Nov 1, 2022Updated 3 years ago
- A study to compare methods for clustering of scRNA-seq data☆46Jul 19, 2024Updated last year
- R package for the joint analysis of multiple single-cell RNA-seq datasets☆220Mar 9, 2026Updated 2 weeks ago
- 10x Genomics Single Cell Analysis☆452Dec 10, 2025Updated 3 months ago
- Inferring CNV from Single-Cell RNA-Seq☆660Nov 14, 2025Updated 4 months ago
- Signature Analysis and Visualization for Single-Cell RNA-seq☆175Jun 10, 2024Updated last year
- scLVM is a modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources…☆110Dec 16, 2022Updated 3 years ago
- Comparison of methods for trajectory inference on single-cell data 🥇☆220Aug 30, 2023Updated 2 years ago
- ☆16Dec 11, 2018Updated 7 years ago