nf-core/scrnaseq

10x Genomics Single Cell Analysis

R toolkit for single cell genomics

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

A list of scRNA-seq analysis tools

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Single-cell analysis in Python. Scales to >100M cells.

scRNAseq analysis notes from Ming Tang

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.

rapids-singlecell: GPU-accelerated framework for scRNA analysis