Results for “atac-seq”

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

ScepticAgent internal architecture reference. Use whenever the user asks how the extension works, wants to add a new AI provider, add a new highlight category, debug communication between components, understand the agent loop or streaming, or work with provider routing and the Gemini CORS proxy.

Append structured execution traces across operational, cognitive, and contextual surfaces with minimal overhead. Load when inspecting agent runs, logging tool calls and observations, enabling post-run debugging, or pairing with structured-planning step IDs. Also triggers on "trace this run", "log execution", "agent observability", "run log", or when fault-localize needs evidence. Default-on during multi-step plans. Traces live at .agent-loom/traces/ — git-ignored by default.

Use `analysis-agent` to analyze permissions, secrets, sensitive data, trust boundaries, and injection; `task-agent` to implement controls; and `review-agent` to assess evidence. Skip self-review and no-trust-impact work.

Predict genome-wide functional genomics tracks from DNA sequence with Borzoi (Linder 2025) — a sequence-to-function model outputting RNA-seq, CAGE, ATAC, and ChIP coverage across long context, used to score non-coding and regulatory variant effects. Use when predicting functional tracks from a DNA sequence, scoring a non-coding/regulatory variant's effect on expression or chromatin, or doing in-silico mutagenesis of a locus. To LOOK UP a variant's population frequency prefer alterlab-gnomad; for its clinical significance prefer alterlab-clinvar; for protein-structure effects prefer alterlab-alphafold; for single-cell foundation models prefer alterlab-scgpt. Part of the AlterLab Academic Skills suite.