Results for “gene-regulatory-networks”

Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

Infer gene regulatory networks (GRNs) from expression matrices using arboreto's scalable GRNBoost2 and GENIE3 tree-ensemble algorithms with Dask-distributed computation. Use when analyzing bulk or single-cell RNA-seq transcriptomics to map transcription-factor-to-target-gene regulatory interactions, build adjacency networks, or run the GRN-inference step of a SCENIC pipeline on large datasets. Part of the AlterLab Academic Skills suite.

Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

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 Open Targets Platform GraphQL API for target-disease associations, tractability and safety data, genetics/omics evidence, and known drugs. Use when identifying or prioritizing therapeutic drug targets, assessing target druggability/safety, or gathering target-disease evidence for drug discovery. Part of the AlterLab Academic Skills suite.

Route research prompts to evidence, retrieval, scraping, data, market, or scientific research skills. Use when prompts mention deep research, current facts, citations, Exa, iterative retrieval, search-first, scraping, data pipelines, PubMed, USPTO, gget, literature review, or scholar evaluation.

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.

NIH grant research skill for clinical researchers. Grill-me intake (research idea + career stage + preliminary data + environment + submission posture + known institute targets) locks down the funding strategy before any search runs. Runs a 5-face...

Guides agents through the full lifecycle of NeMo-RL experiments: understanding recipes, launching reproducible runs, analyzing results, and preserving human oversight with git and TSV logs.

Finetunes the NV-Generate-CTMR MR-brain diffusion UNet from user-supplied NIfTI training volumes using a wrapper that stages configs and delegates to upstream scripts.

Manages GenAI tuning jobs in Agent Platform by listing, inspecting, or canceling ongoing model tuning jobs.

Routes NuRec/Neural Reconstruction requests to the correct upstream NVIDIA skill (datasets, conversion, training, rendering, object harvesting, frame cleanup).

Plans, configures, and manages GKE networking including private clusters, VPC-native configurations, Gateway API, DNS, ingress/egress, Dataplane V2, and IP planning.

Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use when identifying cancer-specific genetic vulnerabilities, finding synthetic lethal interactions, checking whether a gene is essential in given cell lines, or validating oncology drug targets. Part of the AlterLab Academic Skills suite.

Orchestrates a complete bulk RNA-seq differential-expression study from raw FASTQ reads through QC, alignment, quantification, differential expression, pathway enrichment, and publication figures.

Probe RAG applications for prompt injection via poisoned retrieved context and embedding manipulation.

NIH grant research skill for clinical researchers. Grill-me intake (research idea + career stage + preliminary data + environment + submission posture + known institute targets) locks down the funding strategy before any search runs. Runs a 5-facet Consensus positioning analysis (with draft Significance/Innovation language), maps the research to the right NIH institutes and study sections via RePORTER, finds NOSIs and funded overlap, and produces an editable Word document (.docx) with budget/scope-aware mechanism recommendations, submission timelines, and a mandatory program officer recommendation. Use when the user asks about research funding or makes any grant-related request (e.g., 'grants for [topic]', 'find grants for my research idea', 'what grants match my research', 'help me find NIH funding', 'grant opportunities for my research'). NIH-only scope — non-NIH funders (PCORI, DOD CDMRP, VA, foundations) are out of scope and flagged at intake.

Expert in building Retrieval-Augmented Generation systems. Masters embedding models, vector databases, chunking strategies, and retrieval optimization for LLM applications.

Machine learning on genomic interval data (BED files) with the geniml Python package — region embeddings (Region2Vec), joint region+metadata embeddings (BEDspace/StarSpace), single-cell ATAC-seq embeddings (scEmbed), consensus peak sets / universes (build-universe), tokenization, BEDshift randomization, and BBClient/BEDbase caching. Use when training or using region/cell embeddings, clustering scATAC-seq, building a tokenization universe from BED collections, or any ML/feature-learning task over genomic regions. NOT for plain interval arithmetic (overlap/intersect/merge counts) — that is gtars, not geniml. Part of the AlterLab Academic Skills suite.

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

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.

Query NCBI Gene via the E-utilities and Datasets APIs, searching by gene symbol or Gene ID and retrieving gene information (RefSeqs, GO terms, genomic locations, associated phenotypes) including batch lookups. Use when resolving gene symbols to IDs, annotating gene lists, or pulling functional and positional gene metadata for downstream analysis. Part of the AlterLab Academic Skills suite.

Query the GTEx (Genotype-Tissue Expression) portal v2 REST API for tissue-specific gene expression (median TPM across 54 human tissues), expression QTLs (eQTLs), and splicing QTLs (sQTLs). Use when checking which tissues express a gene, finding which gene a non-coding/GWAS variant regulates via eQTLs, or interpreting variant regulatory effects across tissues. NOT for curated trait-variant associations (use alterlab-gwas), population allele frequencies or variant constraint (use alterlab-gnomad), or gene/transcript structure and ID mapping (use alterlab-ensembl). Part of the AlterLab Academic Skills suite.

Graph-based drug discovery toolkit. Molecular property prediction (ADMET), protein modeling, knowledge graph reasoning, molecular generation, retrosynthesis, GNNs (GIN, GAT, SchNet), 40+ datasets, for PyTorch-based ML on molecules, proteins, and biomedical graphs.

Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results. Covers over-representation analysis (ORA), Gene Set Enrichment Analysis (GSEA), and single-sample scoring using gseapy, g:Profiler, and Enrichr libraries.

Scaling Laws for Neural Language Models

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.

Performs differential expression analysis on bulk RNA-seq or pseudo-bulk count matrices with QC, PCA, and contrast testing.

Toolkit de alta performance para análise de intervalos genômicos em Rust com bindings Python. Use ao trabalhar com regiões genômicas, arquivos BED, tracks de cobertura, detecção de sobreposições, tokenização para modelos de ML, ou análise de fragmentos em genômica computacional e aplicações de aprendizado de máquina.

Annotates single-cell RNA-seq data by scoring marker genes, transferring labels with CellTypist, or reasoning over marker lists with an LLM.

Query gnomAD (Genome Aggregation Database) for population allele frequencies and gene constraint scores (pLI, LOEUF) reflecting loss-of-function intolerance. Use when checking how common a variant is across populations, filtering rare-disease candidate variants, assessing variant pathogenicity, or identifying loss-of-function intolerant genes. Part of the AlterLab Academic Skills suite.

Search the Federal Register for rules, proposed rules, notices, and presidential documents, and monitor regulatory activity.

Annotates single-cell RNA-seq data by scoring marker genes, transferring labels with CellTypist, or reasoning over cluster markers with an LLM.

Universal transformation λ(ο,K).τ with recursive self-improvement. USE WHEN routing reasoning, validating knowledge graphs, preparing CICM/ANZCA examinations, or when self-improvement of reasoning/architecture/context is required. Routes queries through R0-R3 complexity pipelines, validates topology (η≥target) and governance (KROG), emits per style (Φ), and compounds learnings into knowledge K. Triggers on complexity assessment, multi-step reasoning, examination mode, or /λ invocation.