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

https://www.sc-best-practices.org

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

A list of scRNA-seq analysis tools

A collection of awesome things regarding all omics.

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.

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

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

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

R package for integrating and analyzing multiple single-cell datasets

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

High dimensional weighted gene co-expression network analysis

DANCE: a deep learning library and benchmark platform for single-cell analysis

Reference mapping for single-cell genomics

R toolkit for the analysis of single-cell chromatin data

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

A tool for semi-automatic cell type classification

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