Bioinformatics AI Agent
Analyze sequencing, transcriptomics, and other omics data using an AI research assistant.
Tool availability is continuously expanding. Request a tool if you don't see what you need.
Quality Control & Preprocessing
Tools
fastqc • multiqc • fastp • cutadapt • trimmomatic • seqtk • sickle-trim • bbmap • sra-tools • entrez-direct • gffread • blast • meme • qualimap • rseqc • quast • pilon
Read Alignment & Mapping
Tools
star • hisat2 • bwa • bwa-mem2 • bowtie2 • minimap2 • bedtools • samtools • bcftools • subread • sambamba • picard • htslib
Quantification & Assembly
Tools
salmon • kallisto • stringtie • rmats • rsem • spades • megahit • flye • velvet • metabat2 • prodigal • prokka • busco
RNA-seq Differential Expression
Tools
deseq2 • edger • limma • tximport • apeglm • variancepartition • dexseq • drimseq
Single-Cell Analysis
Tools
scanpy • anndata • scvelo • scvi-tools • celltypist • squidpy • seurat • monocle3 • soupx • signac • archr • sctransform • harmony • batchelor • mofa2 • scran • scater • scuttle • scdblfinder • dropletutils • slingshot • mast • singler • celldex
Survival Analysis
Tools
survival • survminer
Proteomics Analysis
Tools
msstats • dep • limma
Spatial Omics
Tools
seurat • semla • giotto • spacexr • squidpy • spatialdata • stlearn • tangram-sc • cell2location • stereoscope • archr • signac • chromvar
Functional Enrichment & Pathways
Tools
clusterprofiler • fgsea • enrichplot • biomart • msigdbr • wgcna • mixomics
Variant Calling & Annotation
Tools
gatk4 • freebayes • varscan • strelka2 • bcftools • vcftools • snpeff • ensembl-vep
Cancer Genomics
Tools
mutect2 • cnvkit • arriba • star-fusion
GWAS & Population Genomics
Tools
plink • plink2 • admixture • qqman
Metagenomics & Taxonomic Profiling
Tools
kraken2 • metaphlan • humann • diamond • kaiju
Virome & Phage Analysis
Tools
virsorter • checkv • pharokka
Phylogenetics & Evolution
Tools
mafft • fasttree • iqtree • raxml-ng • orthofinder • trimal • ete3 • dendropy
ChIP-seq / ATAC-seq
Tools
macs2 • diffbind • chipseeker • deeptools
Visualization & Reporting
Tools
ggplot2 • pheatmap • complexheatmap • igraph • enrichplot • cowplot • ggrepel • patchwork
Drug Design & Cheminformatics
Tools
autodock-vina • smina • meeko • rdkit • openbabel • gypsum_dl • admet-ai • fpocket • pymol • plip • prolif • gromacs • openmm • mdanalysis
Integrated Knowledge Sources
Pipette seamlessly connects to leading biological databases, enabling you to enrich your analyses with literature, annotations, variants, structures, and clinical data - all through natural language queries.
Literature & Publications
PubMed
Search biomedical literature, research papers, and scientific publications with advanced query syntax.
Example: "Find recent papers about CRISPR gene editing"Clinical Data & Trials
ClinicalTrials.gov
Access information about clinical trials, including recruitment status, phases, conditions, and interventions.
Example: "Find recruiting cancer trials in phase 3"OpenFDA
Query FDA data on drug adverse events, recalls, and safety information from regulatory databases.
Example: "Find adverse events for Lipitor"Genomic Variants & Mutations
ClinVar
Clinical interpretation of germline variants with pathogenicity classifications and disease associations.
Example: "Find pathogenic BRCA1 variants"dbSNP
Comprehensive database of single nucleotide polymorphisms and short genetic variations.
Example: "Find common SNPs in TP53"gnomAD
Population-scale genomic data with allele frequencies across diverse populations.
Example: "Get allele frequencies for BRCA2 variants"GWAS Catalog
Curated collection of genome-wide association studies linking variants to traits and diseases.
Example: "Find GWAS studies for Type 2 diabetes"Gene & Protein Information
UniProt
Comprehensive protein sequence and functional information database.
Example: "Get information about human insulin protein"Ensembl
Genome annotations, gene coordinates, variants, and comparative genomics data.
Example: "Get information about the BRCA2 gene"UCSC Genome Browser
Access genomic sequences, coordinates, and annotations from the UCSC database.
Example: "Get DNA sequence of chr17:43000000-43100000"Protein Structures
AlphaFold
AI-predicted protein structures with confidence scores and downloadable models.
Example: "Get AlphaFold structure for human p53"Gene Expression & Multi-Omics
GEO (Gene Expression Omnibus)
Repository of high-throughput gene expression and genomics datasets (GSE/GSM accessions).
Example: "Find RNA-seq datasets for breast cancer"cBioPortal
Cancer genomics data from TCGA and other studies, including mutations and expression profiles.
Example: "Find TP53 mutations in lung cancer"Drug Discovery & Therapeutics
Open Targets
Evidence-based drug target identification and disease associations for therapeutic development.
Example: "Find drug targets for Alzheimer's disease"How it works: Simply ask Pipette in natural language, and it automatically determines which database to query, formulates the optimal search, and integrates the results into your analysis.
No API keys, no complex syntax - just ask and receive.
From Results to Discovery
Pipette doesn't stop at delivering results — it helps you decide what to investigate next. After each analysis, the agent reviews your outputs, connects key findings to published literature, and generates testable hypotheses grounded in real science.
Each hypothesis comes with concrete follow-up computational experiments you can run immediately, turning a single analysis into a springboard for discovery. This closes the loop between data and insight, making Pipette a true research partner rather than just a pipeline runner.
Hypothesis Generation
exampleJust ask
Transparent, Reproducible, Scalable
Every analysis on Pipette.bio automatically generates a provenance record - capturing versions, parameters, and outputs in a structured format. You can always trace, reproduce, or share your results with full confidence.
Provenance Snapshot
completedExample of a provenance record automatically generated after each run - concise, human-readable, and machine-traceable.