Results for “genome-scale-model”

Simulates meiotic recombination to produce offspring genomes from parent pairs, modeling Mendelian segregation, de novo mutation, sex determination, trait inference, and clinical evaluation against a disease registry.

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

Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores, drug sensitivity data, and gene effect profiles to identify cancer-specific vulnerabilities, synthetic lethal interactions, and validate oncology drug targets.

Train unsupervised machine learning models on genomic interval data from BED files, including region embeddings, single-cell ATAC-seq analysis, and consensus peak building.

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

Trains machine learning models on genomic interval data from BED files, including region embeddings, single-cell ATAC-seq analysis, and consensus peak building.

Infer gene regulatory networks from gene expression data using scalable algorithms (GRNBoost2, GENIE3) with support for distributed computation.

Query the Cancer Dependency Map (DepMap) for CRISPR gene dependency scores, drug sensitivity data, and gene effect profiles to identify cancer-specific vulnerabilities, synthetic lethal interactions, and validate oncology drug targets.

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.

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

Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for identifying cancer-specific vulnerabilities, synthetic lethal interactions, and validating oncology drug targets.

Computes HEIM diversity and equity metrics from VCF or ancestry data, generating heterozygosity, FST, PCA plots, and a composite HEIM Equity Score with markdown reports.

Provides a standardized interface for ingesting raw data across domains such as genomics, network analysis, document review, and spatial mapping, converting it into semantic vectors for agent use.