Best practice RNA-Seq analysis pipeline for reference-based RNA-Seq analysis
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May 17, 2021 - Shell
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rnaseq-analysis
Here are 43 public repositories matching this topic...
(formerly eelpond) an automated RNA-Seq workflow system
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Oct 14, 2020 - Python
A comprehensive pipeline for RNAseq data analysis
bioinformatics rna-seq gene-expression bioinformatics-pipeline rnaseq rna rna-sequencing rna-seq-analysis bioinformatics-analysis rnaseq-pipeline rnaseq-analysis transcriptome-analysis
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Aug 31, 2024 - Shell
Code, documentation, and tutorials for the DGD model trained on bulk RNA-Seq data.
rna-seq neural-network rnaseq rna-seq-analysis deep-generative-model deep-generative-models rnaseq-analysis deep-generative-modelling
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Jul 20, 2026 - Python
Flujos de trabajos desarrollados y automatizados en el Intituto Nacional de Medicina Genómica para el procesamiento de datos genómicos y transcriptómicos.
dockerfile bioinformatics somatic-variants variant-calling differential-expression genomic-data-analysis nextflow-pipeline rnaseq-analysis transcriptome-analysis
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Apr 8, 2026 - Nextflow
Docker Integrated Comparison of Alternative Splicing (AS) Tools. Benchmarking AS tools and genomic alignment tools.
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Jan 5, 2023 - Python
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.
bioinformatics bioinformatics-pipeline rnaseq rna-sequencing bioinformatics-analysis rna-seq-pipeline rnaseq-analysis
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Dec 14, 2025 - R
Transcriptomics and phenotypic analysis of a cohort of ME/CFS patients.
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Jun 17, 2026 - CSS
A reproducible RNA-seq analysis pipeline built with Snakemake, supporting QC, alignment, quantification, and differential expression.
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Dec 22, 2025 - R
Scripts developed during my master’s program for RNA-seq analysis.
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Dec 17, 2024 - R
The TRMRNASeqTools is a SHELL and Python based pipeline designed for automatic general analysis for TRM sRNA sequencing data in supported plants.
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Sep 23, 2025 - Python
Analysis and metadata for the transcriptome analysis of Schistocerca phase transition
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Apr 9, 2026 - R
Guide and links related to bulk and single-cell RNA-Seq experiments.
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May 3, 2026 - TeX
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Mar 16, 2026 - HTML
This repository includes scripts for RNAseq analysis
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Mar 9, 2026 - R
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.
docker plotly data-visualization webapp rnaseq html-css-javascript publication-quality-plots rshinyapp rnaseq-analysis
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Apr 21, 2025 - R
RNA-seq benchmarking toolkit including UTR annotation, quantification (STAR+Salmon, Salmon, Kallisto), multimapping evaluation, and optional simulation scripts.
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Mar 7, 2026 - Shell
Simple Snakemake RNA-Seq pipeline
python rna-seq snakemake r pandas python3 bioconductor salmon miniconda dge miniconda3 dge-analysis salmon-deseq2 rnaseq-pipeline snakemake-pipeline rnaseq-analysis snakemake-rna-seq
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Mar 21, 2023 - Python
A script to analyze with DESeq2 data from Kallisto. You maybe are interested only in DESeq2 part and its analisis and representation :)
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Jul 24, 2022
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