Biology & Genomics

Filter SNP and indel calls with VQSR, hard filters and bcftools expressions

Jointly genotype GVCFs across cohorts with GATK CombineGVCFs and GenotypeGVCFs

Call structural variants from short reads with Manta, Delly and LUMPY

Normalize indels and split multiallelic variants with bcftools norm

Inspect and query VCF and BCF variant files with bcftools and cyvcf2

Merge, sort, intersect and subset VCF files with bcftools

Summarize VCF quality, sample concordance and stats with bcftools

Dock compound libraries into a protein site with AutoDock Vina and rank them

Analyze living systems through evolution, molecular biology and ecology lenses

Run multi step biomedical research tasks across genomics and drug discovery

Use Biopython for sequences, PubMed queries, BLAST, PDB files and phylogenetics

Query UniProt, KEGG, ChEMBL, PubChem and Reactome through one Python API

Predict protein complex and protein ligand structures with the open Boltz model

Design all atom protein binders around ligands with the BoltzGen diffusion model

Remove batch effects from merged bulk RNA-seq cohorts with pyComBat

Estimate cell fractions in bulk RNA-seq and generate synthetic single cell data

Run PyDESeq2 differential expression with ID mapping and fold change filters

Run bulk RNA-seq differential expression and enrichment in omicverse

Build co-expression modules and hub genes from expression matrices with WGCNA

Fill gaps in single cell trajectories by generating cells from bulk RNA-seq

Optimize cell free protein synthesis yield and troubleshoot aggregation

Query CELLxGENE Census single cell data by cell type, tissue and disease

Predict protein complex and ligand structures with the Chai-1 model

Search ChEMBL for compounds, bioactivity values and SAR data for drug discovery

Search the ChEMBL bioactive molecules database with plain language queries

Handle SMILES, descriptors, fingerprints and conformers with a simple RDKit wrapper

Train molecular machine learning models for ADMET and toxicity with DeepChem

Run SRA download, FASTQ QC, STAR alignment and kallisto quantification pipelines

Search protein structures by 3D similarity in PDB and AlphaFold databases with Foldseek

Run quick BLAST and gene lookups across Ensembl, AlphaFold and Enrichr with gget

Load pathway gene sets correctly and run GSEA enrichment in OmicVerse

Query GTEx for tissue expression, eQTLs and sQTLs to link variants to genes

Search nine genomic databases for variant associations across GWAS and eQTL sources

Tile and segment gigapixel histopathology slides with tissue masks in Python

Query InterPro for protein domain, family and functional site annotations

Rank protein binder designs from AlphaFold, Boltz and BindCraft outputs by ipSAE

Search JASPAR transcription factor motifs and scan DNA for binding sites

Query Labstep electronic lab notebook experiments, protocols and inventory

Design protein sequences around ligands, enzyme active sites and metal sites

Run single-cell and bulk RNA-seq analysis, QC and dataset discovery with Lobster AI

Process mzML and MGF mass spectra and score spectral similarity for metabolomics

Run multi-step omics analyses for therapeutic discovery with code and literature

Query ChEMBL, PubMed, ClinicalTrials.gov and OpenTargets for drug repurposing research

Query the Monarch graph for disease, gene and phenotype links across species

Search Open Targets for drug-disease associations and target validation evidence

Write Opentrons Protocol API v2 scripts for liquid handling and lab modules

Analyze whole slide and multiplex imaging data with nucleus segmentation and graphs

Download and analyze protein structures, chains and metadata from RCSB PDB

Plan end-to-end protein design pipelines with tool choices and compute estimates