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Normalize read-depth copy-ratio profiles and segment them into copy-number regions using circular binary segmentation (CBS, DNAcopy), hidden Markov models, HaarSeg, and fused-lasso methods. Covers GC-content, mappability, and replication-timing (wave-artifact) bias correction, panel-of-normals/PCA denoising, diploid-baseline centering, and algorithm selection by sequencing depth and event size. Use when choosing a segmentation algorithm, correcting depth bias, diagnosing oversegmentation or a mis-centered baseline, tuning CBS or HMM parameters, or understanding why a downstream CNV caller produced fragmented or shifted segments.

日本語の概要は準備中です。原文の説明を表示しています。

Profiles RNA-binding protein targets without antibody or UV crosslinking using STAMP (APOBEC1-RBP fusion, C-to-U editing), scSTAMP (single-cell), TRIBE/HyperTRIBE (ADAR-RBP, A-to-I editing), DART-seq (APOBEC1-YTH for m6A), or Bullseye/SAILOR edit-site detection pipelines. Use when antibody is unavailable or specificity is doubtful, when single-cell RBP profiling is needed (scSTAMP), or when in vivo RBP profiling without UV is preferred.

日本語の概要は準備中です。原文の説明を表示しています。

Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft motif syntax from ChIP-nexus), chromBPNet (Pampari A et al 2025 Nat Genet; bias-factorized base-resolution profiles), EnFormer (Avsec 2021 Nat Methods 18:1196; 196 kb input, ~100 kb effective receptive field), DeepSEA (Zhou 2015; multi-task CNN), and JASPAR 2026 deep-learning collection (1259 BPNet ChIP models). Performs in silico mutagenesis for variant-effect prediction, DeepLIFT/Grad attribution, and TF-MoDISco motif discovery from attribution scores. Use when predicting variant effects on TF binding, discovering soft motif syntax / cooperativity, integrating ChIP-seq with sequence-only predictions, or applying precomputed JASPAR Deep Learning models to new variants.

日本語の概要は準備中です。原文の説明を表示しています。

Builds QSAR / QSPR models using chemprop D-MPNN, MolFormer, Uni-Mol, ChemBERTa, random forest baselines, and Gaussian processes with explicit handling of OECD 5 principles, applicability domain (kNN, leverage, conformal prediction, Mahalanobis), scaffold-balanced splits, ensemble uncertainty, calibration (Platt, isotonic), feature importance (SHAP, atomic attribution), and prospective validation. Use when building target-specific predictive models from in-house bioassay data, ADMET endpoints, or selectivity profiles.

日本語の概要は準備中です。原文の説明を表示しています。

Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when identifying open chromatin from aligned ATAC-seq, choosing between point-source vs HMM peak callers, applying ENCODE-style pseudoreplicate IDR, removing blacklist regions, or fixing 501bp consensus peaks for downstream differential analysis.

日本語の概要は準備中です。原文の説明を表示しています。

Sequence-based deep learning for ATAC-seq using chromBPNet, BPNet, scBasset, or EnFormer. Use when correcting Tn5 bias with neural networks beyond k-mer models, predicting per-base accessibility profiles, scoring in silico variant effects at GWAS or rare-variant SNPs, discovering motifs via DeepLIFT/TF-MoDISco from a trained model, or generating cell-type-specific accessibility predictions for unobserved cell states.

日本語の概要は準備中です。原文の説明を表示しています。

Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.

日本語の概要は準備中です。原文の説明を表示しています。

Audit required bioinformatics command-line tools against Lmod or Environment Modules on Linux HPC clusters, resolve executable and version requirements, and reproducibly deploy missing software through a site-approved EasyBuild, Spack, Bioconda/micromamba, Apptainer, binary, or source-build workflow. Use when Codex must inspect module availability, diagnose a missing or wrong-version bioinformatics tool, install scientific software on Slurm/PBS clusters, publish or validate modulefiles, or produce an auditable and rollback-ready cluster software deployment.

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View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignment file structure.

日本語の概要は準備中です。原文の説明を表示しています。

Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionaries.

日本語の概要は準備中です。原文の説明を表示しています。

Track and report progress of a request to create and run an EcoSIM case for a site ("create an ecosim run for site US-UMB", "set up and run EcoSIM at <site>"). Records four stages — data preparation, namelist creation, model simulation, and output evaluation — in result/<SITE_ID>/progress.json and PROGRESS.md, derives step status from files and quality reports on disk, and records manual results such as the executable, test run, and evaluation verdicts. Use at the start of such a request, after each stage, and whenever the user asks where a site run stands.

日本語の概要は準備中です。原文の説明を表示しています。

Guides agents through scorecards, outcomes, model profiles, and eval suites. Use when running /cc-scorecard or /cc:scorecard, measuring a deliverable, or checking workflow gates with suite-run.

日本語の概要は準備中です。原文の説明を表示しています。

Orientación legal y guía de procesos contractuales para el equipo de Vambe (Chile/MX). Usar SIEMPRE ante preguntas legales o de contratos: 'quiero enviar un contrato', 'cómo mando el NDA', 'el cliente quiere cambios', 'cliente M vs L', '¿me pueden demandar?', 'el cliente no paga', 'cómo finiquito a un empleado', 'protección de datos', 'qué le digo al cliente sobre sus datos', 'nos acusan de incumplimiento', 'me llegó carta de abogados', 'quién puede firmar', 'quién es dueño del código', o cualquier consulta sobre contratos, NDAs, reclamos, laboral, RRHH, PI o cumplimiento normativo.

日本語の概要は準備中です。原文の説明を表示しています。

Aplica el branding de Vambe a PPTX, DOCX, XLSX y HTML. Usa al crear presentaciones, Word, Excel o páginas con identidad visual de Vambe, o si pide "hacerlo bonito" / "estilo Vambe".

日本語の概要は準備中です。原文の説明を表示しています。

Build and sharpen a project's domain model. Use when discussing codebase terminology, writing or editing a GLOSSARY.md, or recording or editing an ADR.

日本語の概要は準備中です。原文の説明を表示しています。

Conduct a retrospective on a coding session.

日本語の概要は準備中です。原文の説明を表示しています。

Import a memory export from another AI assistant into Claude's memory — conversationally, additively, and with the content treated as data.

日本語の概要は準備中です。原文の説明を表示しています。

Construye o actualiza el corpus y el perfil técnico de un reviewer real a partir de sus comentarios en PRs de GitHub. Usar cuando se pida "crear el agente reviewer de X", "armar el perfil de X", "actualizar el corpus de X", "agregar el frontend al perfil de X", o "/generate-github-coder-profile <dir> <Nombre> <login>".

日本語の概要は準備中です。原文の説明を表示しています。

Grill the user relentlessly about a plan, decision, or idea. Use when the user wants to stress-test their thinking, or uses any 'grill' trigger phrases ("grill me", "grill with docs").

日本語の概要は準備中です。原文の説明を表示しています。

Revisa cambios de performance de queries ClickHouse y Postgres (vambe-datascience, CRM, réplicas) contra los errores y aprendizajes de la ronda

日本語の概要は準備中です。原文の説明を表示しています。

Shared vocabulary for designing deep modules. Use when the user wants to design or improve a module's interface, find deepening opportunities, decide where a seam goes, make code more testable or AI-navigable, or when another skill needs the deep-module vocabulary.

日本語の概要は準備中です。原文の説明を表示しています。

Scan a codebase for deepening opportunities, present them as a visual HTML report, then grill through whichever one you pick.

日本語の概要は準備中です。原文の説明を表示しています。

Find root cause of errors, crashes, regressions, failing tests before any fix. Not for code review or new features.

日本語の概要は準備中です。原文の説明を表示しています。

Prepare a private handoff to continue a task in Claude Code, Codex, or another agent; resume from an existing handoff without changing Git or executing its commands automatically. Use for "continue in Codex", "pasar a Claude", "migrar esta sesión", or "retomar este handoff".

日本語の概要は準備中です。原文の説明を表示しています。