Tagged bioinformatics

Infer gene regulatory networks from expression data with GRNBoost2 and GENIE3

Run NVIDIA BioNeMo models for protein folding, docking and molecule design

Query 40+ bioinformatics databases like UniProt and KEGG in one Python API

Run bulk RNA-seq from raw FASTQ through QC, alignment and gene counts

Detect somatic mutations, copy number and tumor purity from cancer sequencing

Query ClinPGx pharmacogenomics for gene-drug interactions and CPIC dosing guidance

Model metabolic networks with flux balance analysis and gene knockouts

Query COSMIC for somatic cancer mutations, gene census and mutational signatures

Predict spatial gene expression from H&E histology slides with DeepSpot-M

Query DepMap for cancer cell line gene dependency and drug sensitivity scores

Predict protein-ligand binding poses with DiffDock from PDB or SMILES input

Draw plasmid maps, sequence logos and GC plots from GenBank and FASTA files

Build and run genomics pipelines and apps on DNAnexus with the dxpy SDK

Fetch DNA and RNA sequences, raw FASTQ reads and assemblies from ENA

Design and embed proteins with ESM3 and ESM C protein language models

Pull ClinGen gene-disease validity and sourced evidence for germline variants

Train region embeddings and consensus peaks from BED genomic interval files

Convert genomic intervals across BED, GFF, VCF and SAM and catch contig mismatches

Predict promoters, splice sites and expression from DNA sequence with hosted models

Run quick CLI and Python lookups for genes, BLAST, AlphaFold and enrichment

Submit protein expression and assay protocols to Ginkgo Cloud Lab robots

Predict N-glycosylation motifs and O-glycosylation hotspots in protein sequences

Analyze genomic intervals, BED coverage and fragments with fast Rust bindings

Process ATAC-seq, ELISA and immunohistochemistry data with curve fitting

Build and deploy Latch bioinformatics workflows with the Latch SDK

Simulate PCR, restriction digests, Gibson and Golden Gate cloning in silico

Run end-to-end protein-ligand docking with pocket detection and pose ranking

Find 1000 Genomes individuals carrying specific variants in a gene or region

Launch nf-core pacsomatic tumor-normal sequencing pipelines from BAM inputs

Run gene set enrichment on gene lists and see which pathways stand out

Query the PrimeKG knowledge graph linking genes, drugs, diseases and phenotypes

Design and validate de novo protein binders with NVIDIA BioNeMo workflows

Draw protein domain maps, contact maps and Ramachandran plots for papers

Find differentially expressed genes from RNA-seq counts with PyDESeq2

Read, write and filter SAM, BAM, VCF and FASTA genomic files in Python

Estimate RNA velocity and cell state trajectories in single-cell data

Fit scVI models for batch correction and multimodal single-cell integration

Predict protein 3D structures from sequence with ESMFold and pLDDT scores

Codon-optimize genes and simulate gene circuits and SBML models

Build graph neural networks for molecules and proteins with TorchDrug

Predict protein and ligand structures and binding affinity with Boltz2 NIM

Score protein designs in a PDB folder for interface pAE, RMSD and designability

Define and validate Proteina-Complexa target sites for protein and ligand binders

Predict small-molecule binding poses against proteins with DiffDock NIM

Generate and analyze DNA sequences with the Evo 2 BioNeMo NIM

Add optional GPU steps to genomics pipelines with NVIDIA Parabricks

Generate protein multiple sequence alignments with the ColabFold MSA-Search NIM

Run a protein structure prediction pipeline from sequence search to folding

Predict monomer protein structures from sequences with the OpenFold2 NIM