GenomifySeq
A free, self-contained desktop app for end-to-end RNA-seq analysis: from raw FASTQ files to differential expression and gene set enrichment. No command-line experience required.
Download for macOS View on GitHub
What it does
- Quantification — runs Salmon on your FASTQ files with automatic sample detection
- Built-in references — download human or mouse GENCODE transcriptomes with one click, or build an index from your own FASTA
- PCA — visualize sample clustering with publication-ready plots
- Differential expression — DESeq2 pairwise comparisons with volcano plots
- GSEA — gene set enrichment analysis using fgsea with any MSigDB GMT file
- Gene set overlay — highlight pathway genes directly on volcano plots
Requirements
- macOS 12 or later (Apple Silicon and Intel)
- ~8 GB free disk space
- 4 GB RAM minimum (16 GB recommended for large transcriptomes)
Installation
- Download the DMG above
- Open it and drag GenomifySeq to Applications
- Launch from Applications — on first run it will install dependencies (~2 GB, one time only)
If macOS blocks the app, go to System Settings → Privacy & Security and click Open Anyway
Support
If you find this useful, consider buying me a coffee ☕