Tagged bioinformatics

Dock small molecules into protein pockets with DiffDock-L blind diffusion docking

Fold proteins, DNA, RNA and ligand complexes with ESMFold2 and ESMC models

Score, embed and generate DNA sequences with the Evo 2 genomic model

Embed proteins and score mutations with Meta's ESM-2 model via fair-esm

Predict protein, nucleic acid and ligand complex structures with OpenFold3

Design protein sequences onto a backbone with ProteinMPNN inverse folding

Embed and annotate single-cell data with the scGPT foundation model

Integrate scRNA-seq batches and transfer cell labels with scVI and scANVI

Design soluble protein sequences that resist aggregation with SolubleMPNN

Look up nutrition facts, protein density and nutrient rankings from USDA data

Extract design tokens, style and visual effects from reference UIs and apply them

Send protein designs to a cloud lab for binding, expression and stability tests

Fetch AlphaFold predicted protein structures and confidence scores by UniProt ID

Read and write AnnData .h5ad files for single-cell analysis with scverse tools

Infer gene regulatory networks from expression matrices with GRNBoost2 or GENIE3

Test whether gene expression or methylation mediates genetic effects on disease

Detect and correct horizontal pleiotropy in Mendelian randomization analyses

Convert gene and protein identifiers and fetch pathways and orthologs via bioDBnet

Search BioGRID ORCS CRISPR screens and retrieve gene scores by organism

Extract the bioinformatics pipeline of a paper and design a customized analysis plan

Map omics findings to diagnostic and therapeutic use cases and audit validation burden

Parse protein PDB and mmCIF structures and compare them with Biopython

Query CZ CELLxGENE Census single-cell expression across tissues, diseases and cell types

Build a ceRNA regulatory network from a gene list using miRNA and lncRNA databases

Run ChEA3 transcription factor enrichment on a gene set and fetch TF metadata

Generate Circos configs for circular genomics plots of variants and networks

Query ClinPGx for gene-drug interactions, CPIC guidelines and allele functions

Call copy number variants from sequencing data and plot genome-wide CNV profiles

Simulate growth, flux and gene knockouts in metabolic models with COBRApy

Plan shared-biomarker studies that link two comorbid diseases through DEGs and hub genes

Plan non-oncology hub gene studies from multi-dataset transcriptome integration

Plan tumor transcriptome studies for prognostic biomarkers and hub genes

Download COSMIC somatic mutation data and cancer gene census for genomic analysis

Find essential and hit genes in pooled CRISPR screens with RRA analysis

Plan studies linking two diseases through shared DEGs, PPI hubs and diagnostic biomarkers

Query CTD for chemical, gene, disease and pathway interactions in toxicogenomics

Convert BAM to bigWig and plot QC and heatmaps for ChIP-seq and ATAC-seq

Screen differentially expressed genes between two groups with volcano and heatmap plots

Predict blind ligand-protein binding poses with DiffDock and confidence scores

Find differentially expressed genes in RNA-seq or microarray data with volcano plots

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

Plan two-disease transcriptome studies with shared biomarkers and hub genes

Plan shared-gene transcriptomic and machine learning studies for two diseases

Select predictive genes with elastic net logistic regression and cross-validation plots

Look up ENCORI miRNA-target and RNA-RNA regulatory interactions

Look up Ensembl genes, sequences and variant effects through the REST API

Generate, predict and embed protein sequences with ESM3 and ESM C models

Interpret FastQC reports for RNA-seq, DNA-seq and ChIP-seq and fix quality issues

Look up NCBI Gene records for symbols and IDs with GO terms and phenotypes