Results for “ncbi-taxonomy”

Manipulate phylogenetic trees, detect evolutionary events, integrate NCBI taxonomy, and create publication-quality visualizations using the ETE toolkit.

Segments abdominal organs from CT NIfTI volumes using the NV-Segment-CT VISTA3D model, producing label maps and structured evidence JSON.

Provides deep generative models for single-cell omics analysis, including probabilistic batch correction, transfer learning, differential expression, and multi-modal integration.

Predicts gene and transcript structure from a DNA sequence using the hosted Genomic Intelligence API, producing a report and JSON output.

Access NCBI GEO (Gene Expression Omnibus) for gene expression and functional genomics data — search and download microarray and RNA-seq datasets by GSE, GSM, GPL, or GDS accession and retrieve SOFT, MINiML, and series matrix files. Use when locating public expression datasets, fetching processed expression matrices, downloading a study's supplementary files, or sourcing per-study transcriptomics data for differential-expression analysis. For raw FASTQ sequencing reads by SRA/ENA run accession use alterlab-ena; for reference tissue-expression baselines (median TPM across human tissues) use alterlab-gtex; for cancer cohort somatic mutations and copy-number use alterlab-cbioportal. Part of the AlterLab Academic Skills suite.

Filters and prioritizes compound libraries in drug discovery using drug-likeness rules, structural alerts, complexity metrics, and a query language.

Analyzes federal contract competitors, incumbents, and obligation trends using live USAspending.gov data via the usaspending MCP, supporting black-hat competitor research and contract-number-first obligation analysis.

Assesses genome, transcriptome, and protein completeness with BUSCO v6, automatically resolving the correct lineage from an organism description and generating reproducible reports.