Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly

A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)

SLAMSeq processing and analysis pipeline

Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.

Nextflow pipeline to processed all RNA-seq data from FAANG

Nanopore transcriptomics workflow with multiple transcript reconstruction options