bio-workflows-rnaseq-to-de

What problem does it solve?

This Skill automates the complex process of analyzing RNA sequencing data, transforming raw FASTQ files into actionable differential expression results, thereby streamlining genomic research.

Core Features & Use Cases

• End-to-End Workflow: Manages the entire RNA-seq analysis pipeline from raw reads to identifying significant gene expression changes.
• Flexible Quantification: Supports both alignment-free (Salmon) and alignment-based (STAR + featureCounts) quantification methods.
• Robust DE Analysis: Utilizes DESeq2 for statistically sound differential expression analysis.
• Visualization: Generates key plots like volcano plots and heatmaps for result interpretation.
• Use Case: Researchers can use this Skill to quickly process their RNA-seq experiments, compare gene expression between different conditions (e.g., treated vs. control), and identify potential biomarkers or therapeutic targets.

Quick Start

Run the RNA-seq to DE workflow on my FASTQ files.