Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

Table of software for the analysis of single-cell RNA-seq data.

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

R package for analyzing single-cell RNA-seq data

R/shiny interface for interactive visualization of data in SummarizedExperiment objects

Bayesian haplotype-based mutation calling

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

R package for integrating and analyzing multiple single-cell datasets

Deep neural networks for predicting CpG methylation

Collection of public scRNA-Seq datasets used by our group

RNA velocity estimation in Python

R package for analyzing and interactively exploring large single-cell RNA-seq datasets

A fast and unsupervised algorithm for spike detection and sorting using wavelets and super-paramagnetic clustering

Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.

A software package for analyzing snapshots of developmental processes

🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version

A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍

R toolkit for the analysis of single-cell chromatin data

Cluster single cells and analyze cell clade relationships with colorful visualizations.

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

A tool that allows to get UMI counts from a single cell protein assay

Multi-sample Unified Discriminant ANalysis

Deep learning for single-cell transcript counts

Color blindness friendly visualization of single-cell and bulk RNA-sequencing data

Fast visualization tool for large-scale and high dimensional single-cell data

Clone identification from single-cell data