Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
A guide to using a Seurat object in conjunction with RNA Velocity
kallisto | bustools workflow for pre-processing single-cell RNA-seq data
Low-compute Nextflow pipeline for single-cell RNAseq QC using pseudo-alignment. Two-mode design: with laptop-friendly quick mode for QC and cost prediction, HPC/cloud full mode for Cell Ranger comparable results. Validated on Element AVITI and Illumina NextSeq 2000 sequencing data using 10X V3 Chromium chemistry. Outputs feed scanpy/Seurat directly
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