Best practice RNA-Seq analysis pipeline for reference-based RNA-Seq analysis

(formerly eelpond) an automated RNA-Seq workflow system

shiny app for WGCNA...

A comprehensive pipeline for RNAseq data analysis

Code, documentation, and tutorials for the DGD model trained on bulk RNA-Seq data.

Flujos de trabajos desarrollados y automatizados en el Inmegen para el procesamiento de datos genómicos y transcriptómicos.

Docker Integrated Comparison of Alternative Splicing (AS) Tools. Benchmarking AS tools and genomic alignment tools.

This repo is a template for running differential gene expression analysis of RNA-seq count data followed by gene set enrichment analysis. This workflow is run in R using Rmarkdown. It is based around the popular R packages, DESeq2, fGSEA, and others.

The TRMRNASeqTools is a SHELL and Python based pipeline designed for automatic general analysis for TRM sRNA sequencing data in supported plants.

Guide and links related to bulk and single-cell RNA-Seq experiments.

A script to analyze with DESeq2 data from Kallisto. You maybe are interested only in DESeq2 part and its analisis and representation :)

bulk-RNAseq analysis for Transcriptomics Course 2021 (MSc Bioinformatics for Computational Genomics)

This project was conducted for the Stanford BioHacks hackathon.

Simple Snakemake RNA-Seq pipeline

Code for Cornel et al., Submitted (2023)

nf-pipeline template for custom data analysis, renders report

Custom workflow for analysis of RNAseq data

IMOM - A pipeline for interacting with, processing, and analyzing multi-OM datasets in phylogenetic and evolutionary context

A book that discusses topics and contains tutorials relevant to population genomics