bioinformatics
124
biopython-phylo
Use Bio.Phylo to read/write phylogenetic trees and perform visualization and statistics; use when tree parsing/conversion, pruning/rerooting, distance calculation, or plotting is required.
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research
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bioinformatics
124
biopython-advanced
Advanced Biopython modules for motifs, population genetics, sequence utilities, restriction analysis, clustering, and GenomeDiagram visualization; use when you need extended bioinformatics analysis beyond basic sequence I/O and alignment.
aipoch
research
bioinformatics
124
microbiome-diversity-reporter
Interpret Alpha and Beta diversity metrics from 16S rRNA sequencing results.
aipoch
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bioinformatics
124
dual-disease-transcriptomic-ml-planner
Generates complete dual-disease transcriptomic + machine learning research designs from a user-provided disease pair. Use when users want to identify shared DEGs, common hub genes, cross-disease biomarkers, or shared molecular mechanisms between two diseases using public GEO data. Triggers: "shared biomarker study for two diseases", "dual-disease transcriptomic ML paper", "identify common DEGs between disease A and B", "cross-disease hub gene discovery", "shared DEG + PPI + ROC design", "immune infiltration shared biomarker", or "I want to study disease X and Y together". Always outputs four workload configurations (Lite / Standard / Advanced / Publication+) with a recommended primary plan, step-by-step workflow, figure plan, validation strategy, minimal executable version, and publication upgrade path.
aipoch
research
bioinformatics
124
biodbnet-api
Access bioDBnet REST services for biological identifier conversion, pathway retrieval, and ortholog mapping. Use when you need to convert gene/protein IDs, find pathways, or retrieve biological annotations via bioDBnet.
aipoch
research
bioinformatics
124
variant-annotation
Query and annotate gene variants from ClinVar and dbSNP databases. \n\.
aipoch
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bioinformatics
124
translational-gap-analyzer
Assess translational gaps between preclinical models and human diseases.
aipoch
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bioinformatics
124
rare-disease-hpo-mapper
Map patient symptoms to Human Phenotype Ontology terms for gene diagnosis.
aipoch
research
bioinformatics
124
string-database
Access the STRING database to map identifiers, retrieve protein–protein interaction networks, and run functional/PPI enrichment when you need interaction context for a gene/protein set.
aipoch
research
bioinformatics
124
patent-landscape
Use when analyzing biotech patent landscapes, identifying white spaces in pharmaceutical IP, tracking competitor patents, or assessing freedom to operate for drug development. Provides comprehensive patent analysis and strategic insights for life sciences innovation.
aipoch
research
bioinformatics
124
gwas-database
Query the NHGRI-EBI GWAS Catalog to retrieve SNP–trait associations, study metadata, and (when available) summary statistics when you need evidence for a variant, trait/disease, gene, or genomic region.
aipoch
research
bioinformatics
124
gene-database
Query the NCBI Gene database via E-utilities and the NCBI Datasets API; use it when you need to search genes by symbol/ID and retrieve annotations (RefSeq, GO, location, phenotype) for single or batch gene lists.
aipoch
research
bioinformatics
124
ensembl-database
Access Ensembl REST API for vertebrate genomic data; use when you need gene/ID lookups, sequence retrieval, variant effect prediction (VEP), or homology/assembly coordinate mapping.
aipoch
research
bioinformatics
124
encori-api
Access ENCORI (StarBase) database for miRNA-target, RNA-RNA, and other regulatory data. Invoke when user asks to search ENCORI or retrieve regulatory interactions.
aipoch
research
bioinformatics
124
ena-database
Access the European Nucleotide Archive (ENA) via REST APIs and FTP/Aspera to search and retrieve sequences, raw reads (FASTQ), assemblies, and metadata when you have accession IDs or need metadata-driven discovery for genomics pipelines.
aipoch
research
bioinformatics
124
bio-ontology-mapper
Map unstructured biomedical text to standardized ontologies (SNOMED CT.
aipoch
research
bioinformatics
124
neuropixels-analysis
End-to-end Neuropixels extracellular electrophysiology analysis (SpikeGLX/Open Ephys/NWB) including preprocessing, motion correction, Kilosort4 spike sorting, QC metrics, and Allen/IBL-style curation; use when processing Neuropixels recordings or when users mention Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, drift/motion correction, or unit curation.
aipoch
research
bioinformatics
124
neoantigen-predictor
Predict neoantigens that may be recognized by the immune system based.
aipoch
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bioinformatics
124
motif-logo-generator
Generate publication-quality sequence logos for DNA or protein motifs.
aipoch
research
bioinformatics
124
spatial-transcriptomics-mapper
Map spatial transcriptomics data from 10x Genomics Visium/Xenium onto.
aipoch
research
bioinformatics
124
sequence-alignment
A skill for performing sequence alignment using NCBI BLAST API. Supports nucleotide and protein sequence comparison against major biological databases.
aipoch
research