single-cell

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

PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.

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

A list of scRNA-seq analysis tools

A collection of awesome things regarding all omics.

Bayesian haplotype-based mutation calling

R package for integrating and analyzing multiple single-cell datasets

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

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.

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

MiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires from any type of sequencing data. Free for academic use only.

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

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

Reference mapping for single-cell genomics

R toolkit for the analysis of single-cell chromatin data

Single cell perturbation prediction

R package for analyzing single-cell RNA-seq data

Collection of public scRNA-Seq datasets used by our group

Graph-linked unified embedding for single-cell multi-omics data integration

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

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

Deep neural networks for predicting CpG methylation

RNA velocity estimation in Python

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

A software package for analyzing snapshots of developmental processes

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.

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.