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Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking, antibody-lot metadata recording, replicate concordance via deepTools multiBamSummary + plotCorrelation, IP enrichment QC via plotFingerprint and per-transcript IP/input ratio distributions, library-complexity saturation curves via PreSeq, and the explicit do-NOT-deduplicate convention for standard non-UMI MeRIP. Use when preparing paired IP and input BAM files for exomePeak2 / MeTPeak / MACS3 peak calling, evaluating MeRIP replicate concordance and IP enrichment, deciding whether to deduplicate (standard MeRIP typically NOT), choosing genome-vs-transcriptome alignment for downstream peak vs m6Anet workflows, recording antibody clone and lot metadata for cross-batch reconciliation, detecting failed IPs via saturation curves and IP/input distribution shape, or generating IP-over-Input bigWig tracks for visualisation.

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Build clustered heatmaps for expression matrices and other features-by-samples data with rigorous distance/linkage/scaling choices, robust color mapping, optimal leaf ordering, and ComplexHeatmap/pheatmap/seaborn rendering. Covers the ward.D vs ward.D2 trap, the row-vs-column scaling decision, multi-track annotations, oncoPrint, and raster rendering for large matrices. Use when visualizing expression patterns across samples or identifying co-regulated clusters.

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Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.

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Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints with explicit choice rules for symmetric vs asymmetric measures, scaffold-hopping vs lead-optimization regimes, activity-cliff diagnosis, and large-library nearest-neighbor methods (BulkTanimoto, MHFP6 LSH forest, USRCAT). Use when ranking compounds by structural resemblance to a query, clustering libraries, finding analogs, or diagnosing activity cliffs.

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Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library complexity. Computes FRiP, NSC/RSC (phantompeakqualtools), library complexity (NRF/PBC1/PBC2), deepTools plotFingerprint (JS distance, AUC, synthetic JS), ChIPQC, IDR with ENCODE Nself/Nt rules, and detects hyper-ChIPable artifacts. Use when validating an antibody, diagnosing failed peak calls, deciding whether to proceed with downstream analysis, grading against ENCODE thresholds, or auditing replicate concordance.

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Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter. Use when characterizing nucleosome organization at promoters and enhancers, calling +1/-1 nucleosomes flanking NFRs, generating V-plots for chromatin structure visualization, or comparing nucleosome positioning between conditions.

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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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Trim PCR primers from aligned reads in amplicon-panel BAMs using samtools ampliconclip. Use when processing SARS-CoV-2 ARTIC, hereditary cancer panels, ctDNA hot-spot panels, or any amplicon assay where primer-derived bases would falsely confirm reference at primer footprints.

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Prove that a command-line tool actually did what it said, instead of trusting its exit code and its output. Snapshots the filesystem before and after, names the expected consequence in advance, and returns one of four verdicts with what could not be seen. Use after running a build, a migration, a scaffolder, a formatter, a codegen step, or an AI coding CLI; when a command printed success and you are about to report "done"; when you are about to write "exit code 0, so it worked"; or when a tool claims it edited files. Needs nothing installed.

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Digital product creation and selling — templates, printables, planners, digital art, delivery setup

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Weekly business retrospective. Reads all snapshots, learnings, skill-usage telemetry, and (if provided) revenue data from the past week. Outputs: what got decided, what shipped, what's stalled, skill activity, suggested next focus. Surfaces unused skills as activation prompts. Use at end of week or end of sprint. Triggered by: 'weekly retro', 'business retro', 'what did we ship', 'how's the week going', '周复盘', '业务回顾', '本周复盘'.

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Author, validate, publish, and test Power BI paginated reports in the RDL format. Automatically invoke when the user mentions "paginated report", "RDL", ".rdl", "Report Builder", "Power BI Report Builder", "SSRS report", "PBIRS", "Power BI Report Server", or asks to "create a paginated report", "build an invoice/statement report", "make a print-perfect report", "connect a paginated report to a semantic model", "edit an RDL file", "publish an .rdl", or "render a paginated report to PDF/Excel".

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Create comprehensive, phased implementation plans with sprints and atomic tasks. Use when user says: "make a plan", "create a plan", "plan this out", "plan the implementation", "help me plan", "design a plan", "draft a plan", "write a plan", "outline the steps", "break this down into tasks", "what's the plan for", or any similar planning request. Also triggers on explicit "/planner" or "/plan" commands.

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Internal implementation skill invoked by /add-native for app-generated PDF report workflows using expo-print and, when present, expo-sharing.

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Use when a UE5 task involves characters in motion: "import FBX from Maya" with a skeleton, "retarget animations", IK Rig, IK Retargeter, feet sinking or floating after retarget, mocap cleanup, Motion Matching, Pose Search, Choosers, GASP, state machine vs motion matching, root motion, offset root bone, foot IK, Control Rig, Animation Blueprint cost, "animation is expensive", budget allocator, URO, MetaHuman LODs, ML Deformer, cloth.

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Use when an agent drives Maxon ZBrush 2026 for any task (sculpt in ZBrush, DynaMesh, ZRemesher, UVs, export, polypaint, posing, 3D print, clean up an AI mesh in ZBrush), when writing ZBrush Python (zbrush.commands) or ZScript, when the ZBrush bridge is not answering, a palette path or set() does nothing, a scripted stroke does not sculpt or a dialog blocks a script, or when a ZBrush result has to be judged the way a professional artist would.

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Use when turning images or photos into 3D meshes with Sparc3D models on Scenario via MCP: single-image or multi-view image-to-3D, watertight meshes for game assets, AR/VR, or 3D printing, mesh-only versus PBR-textured output, face count targets, resolution tiers, or reconstructing human heads and busts with the Portrait variants. Keywords: Sparc3D 2.1 and 2.0, Hitem3D, image to 3D, img23d, multiview, watertight, PBR, GLB, OBJ, STL, FBX.

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Manage Home Assistant configuration safely and fast — edit and deploy YAML (automations, blueprints, scripts, scenes, templates, MQTT), validate with ha core check, deploy via git or rapid scp, reload-vs-restart correctly, verify changes from logs, traces and entity state, and build Lovelace dashboards. Use for any Home Assistant config, automation, template, or dashboard work over SSH/hass-cli/MCP.

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Workflow skill for KiCAD PCB layout and routing via MCP tools. Triggers on: "layout the board", "route traces", "PCB", "place footprints", "copper pour", "board outline", "differential pair", "board setup", "track width", "via", "zone", "design rules", "stackup", "silkscreen".

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Triage technical SEO findings from Ahrefs Site Audit (and similar crawlers) by SEO impact, not just severity. Use this skill when reviewing crawl results, prioritizing technical fixes, scoping a technical SEO sprint, or after running any site-wide crawl. Triggers on site audit results, technical fix list, crawl errors, technical SEO triage, prioritize technical issues, what should we fix first, broken links, redirect chains. Also triggers when a long list of crawler issues is creating decision paralysis.

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Search and retrieve preprints from the bioRxiv repository

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Search and retrieve preprints from the arXiv repository

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Sprint retrospective facilitation

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Integrates with Atlassian products to manage project tracking and documentation via MCP protocol, including Jira issue management, Confluence page editing, sprint and backlog management.

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。