Results for “genetic-data”

Query 20+ bioinformatics databases from the command line or Python for gene information, sequences, protein structures, enrichment analysis, and more.

Create, read, manipulate, and store annotated data matrices using the AnnData Python package, designed for single-cell genomics and general-purpose annotated data workflows.

Quickly query genomic reference databases for Ensembl IDs, gene metadata, sequences, BLAST searches, and enrichment analysis using the gget CLI or Python package.

Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data, enabling efficient access to cell metadata, gene expression slices, summary counts, and embeddings without downloading whole datasets.

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

Query cBioPortal via its keyless REST API for cancer genomics across TCGA, GENIE, MSK-IMPACT and hundreds of studies — somatic mutations, copy-number alterations (GISTIC), mRNA/protein expression, structural variants, and patient-level clinical/survival data. Use when asked how often a gene is mutated/amplified/deleted in a tumor type, to profile oncogenes or tumor suppressors across cancers (pan-cancer alteration frequency), to pull patient-level mutations joined to OS/clinical outcomes, or to validate a cancer target from cohort genomics. For germline variant pathogenicity use alterlab-clinvar; for mutational-signature (SBS) decomposition use alterlab-cosmic; for CRISPR/RNAi gene-dependency use alterlab-depmap; for aggregated target-disease evidence use alterlab-opentargets. Part of the AlterLab Academic Skills suite.

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.

Manages annotated data matrices for single-cell genomics, covering creation, I/O, concatenation, and manipulation of AnnData objects in h5ad and zarr formats.

Queries 20+ bioinformatics databases from the command line or Python for gene info, sequences, BLAST/BLAT, protein structures, viral data, and expression metrics.

Reimplements DnaSP 6 for population genetics analysis of aligned DNA sequences, including nucleotide diversity, haplotype statistics, neutrality tests, linkage disequilibrium, recombination, mismatch distribution, InDel polymorphism, between-population divergence, outgroup-based tests, HKA test, McDonald-Kreitman.

Builds a scheduled, AI-powered data collection agent that scrapes public sources, enriches results with Gemini Flash, and stores them in Notion, Sheets, or Supabase.

Query the 1000 Genomes Project dataset at the individual participant level to find variants, carriers, and relatedness information.

Performs HLA allele genotyping from WGS/WES VCF data, producing a structured markdown report and machine-readable JSON results.

Scores genetic compatibility between all male-female pairings in a Genomebook generation, ranking optimal mating pairs based on heterozygosity, trait complementarity, and disease risk.

Generates a personalised nutrition report from consumer genetic data (23andMe, AncestryDNA, VCF) by interrogating nutritionally-relevant SNPs and producing actionable dietary guidance, all computed locally.

Computes phylogenetic distance matrices and trees from genomic VCF or FASTA data using the fastreeR hybrid Java/Python toolkit.