# Pipette.bio

> Pipette.bio is a cloud-based AI agent for bioinformatics. Researchers upload sequencing files (FASTQ, BAM, h5, CSV) and chat in plain English to run full analysis pipelines — no coding required. It delivers figures, tables, reports, and actionable hypotheses automatically.

## Key Facts

- URL: https://pipette.bio
- App: https://app.pipette.bio
- By: Variome Analytics (https://www.variomeanalytics.com)
- Founded by: Dr. Chirag Gupta (20+ years in computational biology)
- Location: Mount Abu, Rajasthan, India
- Contact: info@pipette.bio
- Free tier: 20 credits/month for 1 year

## How It Works

1. **Upload** — Drop FASTQ, BAM, h5, or CSV files into a cloud workspace (100 GB per session, 200 GB persistent storage).
2. **Ask** — Describe the analysis in plain English. Pipette designs and runs the pipeline automatically.
3. **Discover** — Receive figures, a detailed report, literature connections, and hypotheses for the next experiment.

## Who It's For

- Wet-lab scientists who generate sequencing data but depend on bioinformatics cores
- Small labs and startups without a dedicated bioinformatician
- Bioinformaticians who want to automate routine pipelines
- Principal investigators who need auditable, reproducible records
- Biotech/pharma teams needing version-tracked workflows

## Supported Analysis Types

- RNA-seq differential expression (bulk and single-cell)
- Single-cell clustering, annotation, trajectory analysis
- ChIP-seq and ATAC-seq peak calling
- Variant calling and annotation
- GWAS and population genomics
- Metagenomics and microbiome analysis
- Cancer genomics (fusions, CNV, somatic mutations)
- Spatial transcriptomics
- Drug design and molecular docking
- Phylogenetics and comparative genomics
- Survival analysis
- Literature review (PubMed mining)

## Tools (100+)

### Quality Control & Preprocessing
FastQC, MultiQC, fastp, Cutadapt, Trimmomatic, Seqtk, BBMap, SRA-tools

### Alignment & Mapping
STAR, HISAT2, BWA, BWA-MEM2, Bowtie2, minimap2, Samtools, BEDtools, Picard

### Quantification & Assembly
Salmon, Kallisto, StringTie, RSEM, rMATS, SPAdes, MEGAHIT, Flye, BUSCO

### RNA-seq Differential Expression
DESeq2, edgeR, limma, tximport, apeglm, DRIMSeq, DEXSeq

### Single-Cell Analysis
Scanpy, AnnData, scVelo, scVI-tools, CellTypist, Seurat, Monocle3, SoupX, Signac, ArchR, Harmony, SingleR, MAST, Slingshot

### Spatial Omics
Seurat, Semla, Giotto, SpaceXR, Squidpy, SpatialData, stLearn, Tangram, Cell2Location

### Variant Calling & Annotation
GATK4, FreeBayes, VarScan, Strelka2, bcftools, VCFtools, SnpEff, Ensembl-VEP

### Cancer Genomics
MuTect2, CNVkit, Arriba, STAR-Fusion

### GWAS & Population Genomics
PLINK, PLINK2, ADMIXTURE, qqman

### Metagenomics
Kraken2, MetaPhlAn, HUMAnN, DIAMOND, Kaiju

### ChIP-seq / ATAC-seq
MACS2, DiffBind, ChIPseeker, deeptools

### Drug Design & Cheminformatics
AutoDock Vina, RDKit, OpenBabel, ADMET-AI, fpocket, PyMOL, PLIP, GROMACS, OpenMM

### Functional Enrichment & Pathways
clusterProfiler, fgsea, BiomaRt, WGCNA, mixOmics

### Phylogenetics
MAFFT, FastTree, IQ-TREE, RAxML-ng, OrthoFinder

## Integrated Knowledge Sources

- PubMed (literature)
- ClinVar, dbSNP, gnomAD, GWAS Catalog (genomic variants)
- UniProt, Ensembl, UCSC Genome Browser (gene/protein info)
- AlphaFold (protein structures)
- GEO, cBioPortal (gene expression)
- ClinicalTrials.gov, OpenFDA (clinical data)
- Open Targets (drug discovery)

## Pricing

Credit-based, pay-as-you-go:

- **Free Tier:** 20 credits/month for 1 year
- **Standard:** $25 for 55 credits
- **Pro:** $50 for 120 credits (8% savings)
- **Power:** $100 for 250 credits (12% savings)
- **Teams:** Custom subscriptions for 2+ seats with private infrastructure

Example cost: Full RNA-seq DE analysis (8 samples, 16 paired-end FASTQs, ~20 GB) = ~30 credits (~$12, ~$1.50/sample).

## Published Use Cases

- [RNA-Seq DE: Rice Salt-Alkali Stress](https://pipette.bio/use-cases/rice-salt-stress.html) — 12 samples, 3,456 DEGs (STAR, HISAT2, DESeq2)
- [Single-Cell: Human Pancreatic Islets](https://pipette.bio/use-cases/single-cell-pancreatic-islets.html) — 1,432 cells, 10 clusters (Scanpy, Leiden, UMAP)
- [DE: Dexamethasone Airway Smooth Muscle](https://pipette.bio/use-cases/dexamethasone-airway-smc.html) — 8 samples, 4,000 DEGs (DESeq2)
- [KRAS Variants & Survival in PDAC](https://pipette.bio/use-cases/kras-pdac-survival.html) — 2,034 patients, Kaplan-Meier analysis
- [PubMed scRNA-seq Lung Cancer TME Review](https://pipette.bio/use-cases/pubmed-scrna-lung-cancer-tme.html) — 10 papers analyzed
- [FOXP2 Comparative Analysis Across Vertebrates](https://pipette.bio/use-cases/the-language-gene.html) — 15 species, phylogenetics
- [Rett Syndrome ClinVar Variant Analysis](https://pipette.bio/use-cases/rett-syndrome-clinvar-variants.html) — MECP2 pathogenic variants + gnomAD frequencies
- [Imatinib BCR-ABL Molecular Docking](https://pipette.bio/use-cases/imatinib-bcr-abl-docking.html) — ADMET, AlphaFold, AutoDock Vina (-9.4 kcal/mol)

## How to Cite

> Pipette.bio — AI Agent for Bioinformatics. Variome Analytics. https://pipette.bio

## Pages

- [Home](https://pipette.bio/)
- [Platform](https://pipette.bio/platform.html)
- [About](https://pipette.bio/about.html)
- [Use Cases](https://pipette.bio/use-cases.html)
- [Pricing](https://pipette.bio/pricing.html)
- [Blog](https://pipette.bio/blog.html)
- [Privacy Policy](https://pipette.bio/privacy.html)
- [Terms of Service](https://pipette.bio/terms.html)
- [Security](https://pipette.bio/security.html)
- [Contact](https://pipette.bio/contact.html)