gcell

ChIP-Atlas epigenome data query using gcell. Use this skill when users ask about: - Finding ChIP-seq, ATAC-seq, or DNase-seq experiments - Searching for transcription factor binding data - Finding histone modification data (H3K27ac, H3K4me3, etc.) - Querying epigenome data by cell type or tissue - Downloading peak files or BigWig coverage data - Enrichment analysis for genomic regions or gene lists Triggers: ChIP-seq, ChIP-Atlas, ATAC-seq, DNase-seq, histone modification, H3K27ac, H3K4me3, transcription factor binding, epigenome, peak data, BigWig, enrichment analysis

Gene annotations and TSS analysis using gcell. Use this skill when users ask about: - GENCODE gene annotations - Transcription start sites (TSS) - Gene coordinates and metadata - Transcript information - Querying genes by genomic region Triggers: gene annotation, GENCODE, TSS, transcription start site, gene coordinates, transcript, GTF

Causal network analysis using gcell. Use this skill when users ask about: - Inferring causal relationships from expression data - LiNGAM causal discovery algorithm - Regulatory network construction - Visualizing causal/regulatory networks Triggers: causal network, LiNGAM, causal inference, regulatory network, causal discovery, gene regulatory network

Cell type regulatory analysis using gcell. Use this skill when users ask about: - Loading pre-inferred cell types (GET model outputs) - Gene-by-motif matrices showing TF influence on genes - Gene Jacobian analysis for regulatory importance - Motif subnet visualization - Cell type-specific gene expression patterns Triggers: cell type, regulatory analysis, gene expression, Jacobian, motif subnet, GET model, TF influence

DNA sequence and motif analysis using gcell. Use this skill when users ask about: - Loading and manipulating DNA sequences - Genome assembly access (hg38, hg19, mm10) - Motif scanning with HOCOMOCO motifs - Working with genomic regions (BED, narrowPeak files) - Transcription factor binding site prediction Triggers: DNA sequence, motif scanning, HOCOMOCO, genomic regions, BED file, narrowPeak, genome, transcription factor binding

Pathway enrichment analysis using gcell. Use this skill when users ask about: - Gene set enrichment analysis - GO (Gene Ontology) enrichment - KEGG pathway analysis - Reactome pathway enrichment - Custom pathway/gene set analysis Triggers: pathway enrichment, GO enrichment, KEGG, Reactome, gene set analysis, functional enrichment, ontology

Protein structure and interaction analysis using gcell. Use this skill when users ask about: - Protein sequences from gene names - AlphaFold2 structure predictions and pLDDT scores - UniProt protein information - 3D protein structure visualization - Protein-protein interactions (STRING database) Triggers: protein structure, AlphaFold, pLDDT, UniProt, protein sequence, 3D structure, protein interaction, STRING