Version 3.0 · RNA-seq Made Simple

RNA-seq Analysis
Made Simple

Complete pipeline from raw FASTQ files to publication-ready figures. No command-line experience required.

📖 View Manual

🍎 macOS · 🪟 Windows · 🐧 Linux

macOS
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Linux
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Features
Everything You Need

Built for biologists and bioinformaticians who want results, not infrastructure.

🧬
Full Pipeline Coverage
13-step guided workflow: QC → trimming → alignment → counting → DESeq2 → publication figures. Nothing missing.
🖥️
Desktop App — No Server
Runs entirely on your machine. No cloud, no subscription, no data leaves your computer.
⚡
Conda Environment Ready
Automatically detects your Miniforge/Miniconda/Anaconda installation. Activates the rnaseq environment seamlessly.
📊
Advanced Statistics
Multi-factor design, batch correction (ComBat-seq, SVA), and GSEA / pathway analysis (GO, KEGG, Reactome).
🎯
Real-time Terminal
Every command runs in a live terminal panel inside the app. Watch STAR alignment progress line by line.
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Cross-platform
Identical experience on macOS, Windows, and Linux. Same interface, same commands, same results.
13-Step Pipeline
From FASTQ to Figures

Each step is fully guided with copy-paste commands and explanation of what to expect.

✓
🩺
System Check
Detect conflicting software and verify your environment before starting.
⚙
⚙️
Configure Project
Set organism, sequencing type, and project name. Generates directory structure.
yeast · human · mouse · fly
1
📦
Install Tools
Install STAR, HISAT2, Salmon, FastQC, Trimmomatic, featureCounts via conda.
conda install
2
⬇️
Download Data
Download reference genome, annotation GTF, and FASTQ files from SRA / ENA.
wget · sra-tools · fasterq-dump
3
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Quality Control
Run FastQC and MultiQC to assess read quality and adapter content.
FastQC · MultiQC
4
✂️
Trimming
Remove adapters and low-quality bases with Trimmomatic or Trim Galore.
Trimmomatic · Trim Galore
5
🧬
Genome & Index
Build STAR or HISAT2 genome index from the reference FASTA + GTF.
STAR --runMode genomeGenerate
6
🎯
Alignment
Align reads to the genome. Produces sorted, indexed BAM files.
STAR · HISAT2 · Salmon
7
#
Gene Counting
Count reads per gene with featureCounts or HTSeq. Produces count matrix.
featureCounts · HTSeq
8
🌿
Gene Family Analysis
Identify gene families, orthologs, and functional groups in your dataset.
9
📊
DESeq2 in R
Differential expression analysis, VST normalization, PCA, volcano plots.
DESeq2 · ggplot2 · pheatmap
10
📈
Plots & Results
MA plots, heatmaps, volcano plots, export to CSV / PDF.
ggplot2 · ComplexHeatmap
+
⚗️
Multi-factor Design & Batch Correction
Advanced: interaction models, ComBat-seq, SVA, limma::removeBatchEffect.
Advanced
+
🌐
GSEA & Pathway Analysis
Gene set enrichment, GO / KEGG / Reactome ORA and GSEA with clusterProfiler.
clusterProfiler · fgsea · ReactomePA
Requirements
What You Need

Install these once, then RNAflow handles everything else automatically.

🐍
Python 3.8+
Used by the local server. Usually pre-installed on macOS and Linux.
📦
Conda (Miniforge)
Required for tool installation. Miniforge is recommended.
→ Download Miniforge
💾
~50 GB Disk Space
For reference genome, index files, FASTQ, BAM, and results.
🧠
8 GB RAM (minimum)
16 GB+ recommended for genome indexing and alignment steps.

Ready to Analyse Your RNA-seq Data?

Runs entirely on your computer. No cloud, no subscription, no data leaves your machine.

Download RNAflow