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

shiny app for WGCNA...

(formerly eelpond) an automated RNA-Seq workflow system

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 Intituto Nacional de Medicina Genómica 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.

A reproducible RNA-seq analysis pipeline built with Snakemake, supporting QC, alignment, quantification, and differential expression.

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

Scripts developed during my master’s program for RNA-seq analysis.

Transcriptomics and phenotypic analysis of a cohort of ME/CFS patients.

No description provided.

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

RNA-seq benchmarking toolkit including UTR annotation, quantification (STAR+Salmon, Salmon, Kallisto), multimapping evaluation, and optional simulation scripts.

Simple Snakemake RNA-Seq pipeline

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

Breast Cancer Survival Prediction

Code for Cornel et al., Submitted (2023)

RNA Sequencing Data Analysis: A 2025 Review and Updated Snakemake Pipeline

A workflow for analysis of paired-end RNA-seq data and differential gene expression analysis.

RNA Sequencing Data Analysis for Beginners

RNA seq analysis coursework that analyses the GSE268197 datasets through differential gene expression and functional enrichment analysis

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

Splicing assembly for non-model organisms using RNAseq data

Set of classes, codes and scripts which I use for Omics data analysis

This repository includes scripts for RNAseq analysis

Custom workflow for analysis of RNAseq data

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

RNAlytics: A Shiny-based web application for RNA-Seq analysis, offering differential expression, KEGG/GO enrichment, and interactive visualizations (PCA, Volcano, Heatmap, Gene Count). Built with R 4.4.3, it provides a user-friendly platform for researchers to explore genomic data. Deployable on Shiny Server for full control and scalability.