Results for “ncbi-blast”

Provides reference documentation and code patterns for Biopython, covering sequence handling, alignments, NCBI database access, BLAST, protein structures, phylogenetics, and other bioinformatics tasks.

Downloads genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools.

Ingests music into a LanceDB via ncmdump-rs and sf-cli, searching and downloading from Netease Cloud Music or Bilibili, decrypting local NCM files, and extracting metadata, lyrics, and cover art.

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

Automates sequencing quality control by running FastQC and MultiQC, extracting quality metrics, and generating publication-ready visualizations via a CLI or MCP stdio server.

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.

Guides analysis of Neuropixels recordings from raw data to curated units, covering preprocessing, motion correction, spike sorting, quality metrics, and export.

Provides Python tools for biological computation, including sequence manipulation, file I/O, database access, structural bioinformatics, and phylogenetics.

Query 40+ bioinformatics services (UniProt, KEGG, ChEMBL, Reactome) with a unified Python interface for cross-database analysis, identifier mapping, and sequence analysis.