Biology & Genomics

Check VCF variant calls against read evidence in BAMs and capture IGV screenshots

Import DRAGEN result bundles from Illumina for local tertiary analysis

Compute polygenic risk scores from a local VCF or WGS file with an MCP server

Query Labstep electronic lab notebook experiments, protocols and inventory

Compute pairwise LD between a lead variant and nearby variants using 1000 Genomes

Render a regional plot to visually check whether two GWAS and QTL signals match

Map marker-dominant regions in spatial data from spot-count CSV files

Run two-sample Mendelian randomization with IVW, Egger and sensitivity checks

Estimate epigenetic age from DNA methylation arrays with PyAging clocks

Combine QC reports from many bioinformatics tools into one MultiQC HTML report

Download NCBI genomes, genes, virus sequences and taxonomy with the datasets CLI

Run nf-core RNA-seq preprocessing from FASTQ or BAM with preflight checks

Run nf-core RNA structure analysis from chemical probing reads to 2D diagrams

Run nf-core Sarek variant calling for germline and somatic sequencing data

Run nf-core single-cell RNA-seq preprocessing from FASTQ with preflight checks

Collect public omics evidence for a drug target to support research triage

Explore organ-specific proteomic aging clocks with per-protein contribution breakdowns

Run gene-set pathway enrichment across KEGG, GO, Reactome and more with charts

Build phylogenetic trees end to end from sequence alignment to ML inference

Fetch proteomics project metadata and raw files from the PRIDE Archive by accession

Estimate organ-specific biological age from Olink proteomic data with elastic net clocks

Run differential expression on label-free MaxQuant and DIA-NN proteomics data

Search and retrieve scientific lab protocols and steps from protocols.io

Simulate offspring genomes from parent pairs with meiotic recombination and mutation

Run differential expression on bulk RNA-seq counts with QC, PCA and contrasts

Flag multi-sample QC outliers for identity, sex, contamination and batch shift

Build batch-aware single-cell latent embeddings with scVI and scANVI

Run a Scanpy single-cell pipeline for QC, clustering, markers and cell-type calls

Run NGS read QC, alignment and BAM processing with FastQC, BWA and SAMtools

Analyze 10x Visium spatial transcriptomics with clustering, markers and spatial stats

Predict protein structures with Boltz-2 or OpenFold3 and extract confidence scores

Score evidence for a drug target and return go or no-go decisions

Fetch regional plasma pQTL summary statistics from UK Biobank proteomics data

Annotate VCF variants with VEP, ClinVar and gnomAD and rank them

Annotate VCF variants with VEP, ClinVar and gnomAD, ranked by impact

Run a pipeline from WGS FASTQ through variant calling to polygenic risk scores

Query TCGA tumor expression, survival and correlation data for genes

Parse FASTA, GenBank and PDB files and query NCBI with Biopython

Search and download 3D protein and nucleic acid structures from RCSB PDB

Track animal poses in video with DeepLabCut, from labeling to behavioral analysis

Browse and filter bioRxiv and medRxiv preprints by date, category and keyword

Build extracellular spike sorting pipelines with SpikeInterface from loading to export

Plan and validate public GEO, SRA, TCGA and GTEx data downloads with manifests

Design human-in-the-loop single-cell RNA-seq QC with per-sample thresholds

Run pathway enrichment, GO analysis and protein interaction networks on gene sets

Work with DNA and protein sequences, BLAST searches and PDB structures in Biopython

Search bioRxiv biology preprints with natural language queries

Query ChEMBL for bioactivity values, compound searches and SAR studies

Look up drug mechanisms, binding affinities and ADMET data from ChEMBL