1.7천건 · 관련도순
集群数据管理 Skill —— 涵盖数据使用规范、压缩优化、数据共享（ACL）、文件扫描与清理、文件完整性校验、genozip 基因组压缩等全流程。Use when the user asks about: managing data on the HPC cluster, compressing genomic files (fq/bam/vcf), sharing data between users/groups, scanning for large files or cleaning up disk space, checking file integrity (md5/gzip/bam), using genozip, checking disk quota, or any data lifecycle management task on the NCPGR HPC cluster.
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WheatOmics 平台（wheatomics.sdau.edu.cn）数据查询技能。当用户需要查询小麦/麦族基因信息、表达谱、共表达、蛋白互作、同源与共线性、序列获取、BLAST、GO/KEGG 富集、变异数据、文献检索或引物设计时使用。
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Test whether two or more traits share a causal variant at a locus using Bayesian colocalization (coloc.abf, coloc.susie, HyPrColoc, moloc, eCAVIAR, SMR/HEIDI, PWCoCo, SharePro). Use when integrating GWAS with eQTL/sQTL/pQTL/mQTL, distinguishing shared causal variants from LD-driven coincidence, handling allelic heterogeneity, choosing between single-causal vs multi-causal methods, picking PP.H4 thresholds, running sensitivity over p12, or harmonising summary statistics for colocalization.
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Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free intron clusters), VAST-TOOLS (cross-species with microexon support), Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage), or IRFinder-S (intron retention coverage-aware). Distinguishes the five canonical event classes (SE, A5SS, A3SS, MXE, RI), special classes (microexons, exitrons, AFE/ALE), intron retention subtypes (canonical RI vs detained introns), and applies effective-length normalization. Use when measuring splice-site usage or isoform inclusion ratios from short-read RNA-seq.
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Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.
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Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment data quality before variant calling or quantification.
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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.
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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.
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Process and analyze single-cell ATAC-seq data with Signac, ArchR, SnapATAC2, or Cell Ranger ATAC. Use when handling 10X scATAC or 10X Multiome (paired RNA+ATAC) data, performing per-cell QC, choosing between ArchR/Signac/SnapATAC2 ecosystems, building per-cluster consensus peaksets, integrating with paired scRNA-seq, doublet detection (AMULET vs ArchR vs scDblFinder), or running pseudobulk differential accessibility per cluster.
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Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection analysis.
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Analyze TF motif accessibility variability across samples or single cells using chromVAR. Use when identifying TF motifs whose accessibility correlates with conditions, computing per-sample motif z-scores after matched background correction, comparing to ArchR / Signac equivalents, or distinguishing motif-accessibility signal from per-site footprinting.
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Azure Monitor OpenTelemetry Exporter for Java. Export OpenTelemetry traces, metrics, and logs to Azure Monitor/Application Insights.
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Reconstruct workflow behind a past coding-agent artifact using local ax sessions/commits/skills/tool traces. Use when asked how X was built.
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The PRIMARY development workflow for the Archon project (remote-coding-agent). Use this skill instead of any PRP skills when working on Archon code. Routes to 10 specialized cookbooks based on what the user is trying to do: RESEARCH — "how does the orchestrator work?", "where is session state defined?", "trace the workflow execution flow", "what is IWorkflowStore?" INVESTIGATE — "should we use Drizzle or Prisma?", "what's the best way to add WebSockets?", "can we migrate to Turso?", "how do other projects handle rate limiting?" PRD — "write a PRD for dark mode", "spec out the notification feature", "product requirements for webhook retry" PLAN — "plan the auth refactor", "design the caching layer", "create an implementation plan for #42" IMPLEMENT — "implement the plan", "execute .claude/archon/plans/auth.plan.md", "build the feature from the plan", "code this up" REVIEW — "review PR #123", "review my changes", "code review the diff" DEBUG — "debug the failing test", "why is streaming broken?", "root cause analysis on the timeout issue" COMMIT — "commit these changes", "commit the auth refactor" PR — "create a PR", "open a pull request for this branch" ISSUE — "report this to gh", "create a gh issue", "log it in github", "file a bug for this", "create a feature request" This skill triggers on ANY development task: researching, investigating, planning, building, reviewing, debugging, committing, or shipping code. NOT for: Running Archon CLI workflows in worktrees (use /archon instead).
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Trace bugs through call chains using knowledge graph
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Use when the user is debugging a bug, tracing an error, or asking why something fails. Examples: "Why is X failing?", "Where does this error come from?", "Trace this bug"
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Use when the user asks how code works, wants to understand architecture, trace execution flows, or explore unfamiliar parts of the codebase. Examples: "How does X work?", "What calls this function?", "Show me the auth flow"
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Independent, traceable code review of one SDD Composy task in review_required against its approved PRD, stories, TechSpec, evidence, and project rules, with stable findings and severities. Use when a task passed QA and evidence — 'revisar a TASK-003', 'code review da task', 'review this task's diff'. Do NOT use for code review outside an SDD workspace (use the host code review), for QA (sdd-qa), or for verification (sdd-verify).
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Read-only consolidated snapshot of an SDD Composy workspace: lifecycle stage, task contracts, trace integrity, loops, fleets, and the next action, without changing any file. Use for 'em que pé está o SDD', 'status do fluxo', 'qual a próxima ação', 'where are we in the workflow'. Do NOT use for git, CI, infrastructure, or other plugins' status, or to change state.
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Deliver a small bounded change inside an initialized SDD Composy workspace through the quick path: at most five implementation files, a registered TASK, TDD, evidence, trace, and a verified verdict, escalating otherwise. Use for a precise objective with no existing task — 'ajuste rápido via SDD', 'quick fix under SDD', 'small change to X in the SDD flow'. Do NOT use for an already registered task (sdd-execute), for architecture, migrations, or destructive work, or in repositories without SDD Composy (other plugins' quick).
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Create or revise the SDD Composy technical specification (tasks/prd-SLUG/techspec.md) from the approved PRD, resolved stories, and mapped codebase, with DEC/RISK and TU/TI/E2E traceability and a human gate. Use when the product contracts are approved and architecture is needed — 'criar a spec técnica', 'techspec do prd-SLUG', 'design the solution for…'. Do NOT use to change product scope, before PRD and stories approval, or for design notes outside SDD.
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Design traceable Web and browser checks with explicit browser coverage, observed interactions, isolated sessions, and evidence limitations.
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Select traceable regression coverage from change impact, affected risks, criteria, dependencies, and prior defects rather than execution convenience.
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Assess requirement clarity, testability, completeness, consistency, and traceability without inventing missing acceptance criteria.
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