Biology & Genomics

Analyze TCR and BCR repertoires for clonality, CDR3 diversity and antigen matches

Explore antibody-antigen binding, MHC prediction and vaccine epitope mapping

Connect diseases, drugs and variants through shared KEGG pathways

Find and read peer-reviewed lab protocols from protocols.io step by step

Identify lipids and map lipid metabolism pathways with LIPID MAPS and HMDB

Test whether an exposure causally affects a disease with Mendelian randomization

Annotate mass-spec metabolite features and search HMDB, MetaboLights and KEGG

Normalize, test and interpret untargeted metabolomics data from mass-spec runs

Map metabolites to pathways and disease links using KEGG, Reactome and MetaCyc

Classify microbiome taxa and genome quality from MGnify and GTDB data

Find and QC microbial genome assemblies from NCBI Datasets for any organism

Profile microbiomes and host-microbe links with MGnify, GTDB and BacDive

Compare genes across model organisms using MGI, ZFIN, FlyBase and WormBase

Design Gibson and Golden Gate assemblies and analyze existing cloning products

Integrate transcriptomics, proteomics and metabolomics into shared pathway results

Identify whether a compound is a known natural product and classify its chemistry

Map compound-target-disease networks for repurposing and off-target predictions

Explore neural circuits and brain disease genetics using the Allen Brain Atlas

Decode fMRI brain coordinates into cognitive terms using Neurosynth studies

Run nf-core RNA-seq, variant calling and ATAC-seq pipelines on FASTQ or GEO data

Predict miRNA targets and lncRNA functions using miRBase, miRDB and LNCipedia

Trace GWAS hits through causal genes and pathways to druggable targets

Find the real protein targets of a peptide from its sequence alone

Run PheWAS across UK Biobank, FinnGen and other biobanks for one variant or gene

Align sequences and build phylogenetic trees with MAFFT, MUSCLE and Clustal

Annotate plant genes and pathways with PlantReactome and Ensembl Plants

Compare allele frequencies, Fst and Hardy-Weinberg tests across populations

Compare variant frequencies across 1000 Genomes superpopulations and samples

Design PCR and qPCR primers with melting temperature and hairpin checks

Run and review iterative protein binder design campaigns across model families

Map protein-protein interaction networks from STRING, BioGRID and Complex Portal

Explain how a missense variant breaks protein function using five evidence layers

Analyze phosphorylation, ubiquitination and other PTM sites with enzymes and motifs

Interpret missense variants by gained or lost ESMC sparse autoencoder features

Annotate each residue of a PDB structure for interface, pocket and burial

Predict protein 3D structures with ESMFold and fetch AlphaFold models

Retrieve protein structures from PDB, AlphaFold and SWISS-MODEL with quality checks

Design protein binders with RFdiffusion backbones and ProteinMPNN sequences

Analyze mass-spec proteomics for differential abundance, PTMs and pathways

Find proteomics datasets in PRIDE, MassIVE and ProteomeXchange with file links

Map TF motifs, cCREs and chromatin accessibility using JASPAR and ENCODE

Score non-coding variants with eQTL, RegulomeDB and CADD evidence

Explain why key protein residues matter using structure and UniProt features

Integrate single-cell data with scVI, scANVI, totalVI and PeakVI models

Retrieve sequences, find orthologs and run FASTQ QC and alignment

Fetch DNA, RNA and protein sequences from NCBI and ENA by accession or gene

Run single-cell RNA-seq QC and doublet detection with scanpy and anndata

Trace compound names to activity, ADMET and purchasable stock with PubChem and ChEMBL

Turn spatial gene expression and domain annotations into tissue-level biology