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)

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

SLAMSeq processing and analysis pipeline

Nextflow pipeline to processed all RNA-seq data from FAANG

Nanopore directRNA (hopefully cDNA too ;)) workflow with many transcript reconstruction alternatives