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

A collection of Galaxy-related training material

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.

Bioconductor cheat sheet

Fast, efficient RNA-Seq metrics for quality control and process optimization

🏃 The go-to single-cell Foundation Model

Transcript quantification import for modular pipelines

Analyze your RNA sequencing data without writing a single line of code

A proof of concept of RNAseq pipeline

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins

A course on genomics and bioinformatics from WashU

gatk4 RNA variant calling pipeline

Compare different differential abundance and expression methods

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Python implementation of bulk RNAseq deconvolution algorithms

Annotation-agnostic differential expression analysis of RNA-seq data via expressed regions-level or single base-level approaches

RNA-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.

R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/