Tagged bioinformatics

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

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

Generate English clinical PDF reports from whole exome sequencing data

Generate Spanish clinical PDF reports from whole exome sequencing data

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

Query TCGA tumor expression, survival and correlation data for genes

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

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

Query the Ensembl genome API for genes, sequences, variants and orthologs

Query NCBI Gene for gene details, RefSeqs, GO terms and batch annotations

Analyze gene expression, BLAST alignments, GWAS results and genome assembly

Trace gene queries through expression analysis to pathway-level interpretation

Search and download NCBI GEO expression datasets for microarray and RNA-seq studies

Map genes to KEGG pathways and convert IDs through the KEGG REST API

Query KEGG for metabolic pathways, compounds, drugs and gene-pathway links

Query NCBI for GenBank sequences, gene summaries, SNPs and literature links

Query Open Targets for gene-disease associations and drug evidence scores

Query the RCSB PDB for protein structure metadata and structure file downloads

Analyze protein 3D structures, homology models, AlphaFold output and docking

Query Reactome for pathway enrichment, gene-pathway mapping and interactions

Run single-cell RNA-seq QC, clustering, UMAP and differential expression

Preprocess single-cell RNA-seq data and annotate cell types with scanpy

Predict fitness effects of single amino-acid substitutions from labeled protein assays

Query STRING for protein-protein interactions and enrichment across species

Search UniProt for protein sequences, FASTA files and ID mapping

Look up UniProt protein sequences, functions and cross-references