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epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models. It contains two separate peak callers, one for consensus peaks from biological or technical replicates, and one for differential peaks from multi-replicate multi-condition experiments. In differential peak calling, epigraHMM provides window-specific posterior probabilities associated with every possible combinatorial pattern of read enrichment across conditions.

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Systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. The HiC-DC+ (Hi-C/HiChIP direct caller plus) package enables principled statistical analysis of Hi-C and HiChIP data sets – including calling significant interactions within a single experiment and performing differential analysis between conditions given replicate experiments – to facilitate global integrative studies. HiC-DC+ estimates significant interactions in a Hi-C or HiChIP experiment directly from the raw con

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topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and

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MHC (major histocompatibility complex) molecules are cell surface complexes that present antigens to T cells. The repertoire of antigens presented in a given genetic background largely depends on the sequence of the encoded MHC molecules, and thus, in humans, on the highly variable HLA (human leukocyte antigen) genes of the hyperpolymorphic HLA locus. More than 28,000 different HLA alleles have been reported, with significant differences in allele frequencies between human populations worldwide

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已有功能的需求变更闭环（门禁式七步）。触发硬条件：要改的功能已经实现并跑起来了。当用户说"改需求""需求变更""调整交互""改功能""重构流程"，或改动容易散到多个文件、碰到鉴权/存储/配置/权限、需要可靠验证 + 回滚方案时使用。流程：锁 scope 写 change brief → 从代码确认当前行为（不靠记忆和假设）→ 影响面与风险评估 + 回滚计划 → 提出新设计等用户批准（**未获批准绝不动代码**）→ 小而局部的 diff → 跑固定回归清单 → 更新文档和决策日志。产出：change brief + 代码 diff + 回归记录 + decision log。不适用于：全新功能从零做（走 issue-pool → page-solution-design（有界面时）→ backend-logic-design（有规则需讨论时）→ prd-test-writer）、只改视觉样式不动任何逻辑（按已有界面直接调整）、新想法还没定要不要做（先用 issue-pool 入池）、写 PRD/测试用例（用 prd-test-writer）、提交推送发版（用 git-push）。注意：本 skill 的七步流程通用于任何项目，但 scripts/impact_scan.sh 与 references/chrome-extension-regression-example.md 是 Chrome 扩展示例；通用回归使用 references/regression-checklist.md，按项目实际选择检查。

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Provides guidance for writing and benchmarking optimized CUDA kernels for NVIDIA GPUs (H100, A100, T4) targeting HuggingFace diffusers and transformers libraries. Kernels must be kernel-builder/ABI3-compliant: no pybind11, no setup.py, TORCH_LIBRARY_EXPAND bindings only. Supports models like LTX-Video, Stable Diffusion, LLaMA, Mistral, and Qwen. Includes integration with HuggingFace Kernels Hub (get_kernel) for loading pre-compiled kernels. Includes benchmarking scripts to compare kernel performance against baseline implementations.

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Provides guidance for writing and benchmarking optimized Triton kernels for AMD GPUs (MI355X, R9700) on ROCm, targeting HuggingFace diffusers (LTX-Video, SD3, FLUX) and transformers. Core kernels: RMSNorm, RoPE 3D, GEGLU, AdaLN. Includes XCD swizzle, autotune, diffusers integration patterns, and LTX-Video pipeline injection.

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Turn a set of commits or a diff into a clean, user-facing changelog entry. Use before a release or PR description.

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Use when positioning needs defining or sharpening — a statement built on Promise, Proof, and Path, a differentiation matrix against competitors, category entry points, a three-level message hierarchy, and tagline directions. Trigger on 'positioning', 'positioning statement', 'what makes us different', 'USP', 'why should customers choose us over them', 'we sound the same as everyone else'. Also use when the user can list features but not a reason to pick them. Not for — competitor teardown research, see `08-competitor-research-global`; how the brand sounds in writing, see `35-brand-voice-global`; the offer and its value stack, see `31-offer-design-global`; the launch built on it, see `59-go-to-market-global`.

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Expert AI art prompt engineer for Midjourney and Stable Diffusion. Generates high-quality prompts including unified batch illustrations, marketing designs, interactive compositions, and structured framework prompts with translations.

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Use this skill whenever the user wants to analyze binaries with radare2/r2 from the command line, including reverse engineering, disassembly, function analysis, strings/import inspection, patching, binary diffing, hex inspection, or r2 scripting. Also use it when the user mentions PE/ELF/Mach-O/DEX/WASM files together with CLI analysis, `rabin2`, `rasm2`, `radiff2`, `r2pipe`, or asks for radare2 command help on Windows/Linux/macOS.

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Creates a Check for Understanding (CFU) for a math topic or standard: 1–3 targeted formative items whose distractors come from documented student misconceptions, plus a teacher guide routing each likely response to a specific next instructional step. Load BEFORE asking any clarifying question about grade, standard, or topic. This skill is for math; for other subjects, help as you normally would and don't mention the skill to the user. Triggers on asks to create, write, generate, or design a check for understanding, formative check, quick check, or exit ticket for a math concept or standard, and on implicit signals like "I need to see who got it before I move on." Not a quiz, test, or practice set — a CFU is read for what it reveals, not scored, so a numbered quiz or a bare answer key is a different job. Does not create a lesson (k12-lesson-plan-creation, which brings its own exit ticket), tier one (k12-lesson-differentiation), or prepare a teacher to teach one (k12-lesson-prep).

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Web change monitoring - track changes on pages, detect updates, changelog diffs

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Security-focused differential code review with blast radius analysis, risk-adaptive depth (DEEP/FOCUSED/SURGICAL), git history correlation, and structured finding format. Adapted from Trail of Bits. Use when reviewing PRs, commits, or code changes for security implications.

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Use the open-source free `cloc` tool for line-count, language-mix, and diff statistics in .NET repositories. USE FOR: repeatable LOC reports; language-mix or branch-diff statistics; codebase size and solution-composition measurements. DO NOT USE FOR: judging developer productivity from raw LOC; replacing behavioral verification, architecture review, or complexity analysis. INVOKES: inspect the repository context, edit targeted files, and run relevant build, test, lint, or validation commands when changes are made.

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Resizes, scales, and adjusts video resolution and dimensions using GPU-accelerated NVENC encoding via Volcengine LAS. Video resizing, video scaling, video upscaling, and video downscaling — change video resolution, enlarge or shrink video dimensions, and adjust video size for different platforms and screens. Video compression by reducing resolution and video transcoding and re-encoding with specific dimension constraints. Supports flexible min/max width and height ranges with aspect ratio preservation strategies (increase, decrease, or disable), including landscape to portrait conversion. Async submit-poll workflow with batch support. Use this skill when the user wants to resize or scale video resolution (upscale/downscale), change video dimensions for different platforms, compress videos by reducing resolution, transcode/re-encode videos with GPU NVENC, adjust aspect ratio including landscape-to-portrait conversion, adapt videos for mobile/web/social media, or batch process multiple videos.

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Generates English pull request titles and bodies by comparing the current branch with main. Use when the user asks to draft PR content, summarize branch changes, or produce a PR title/body from git diff.

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Builds a positioning canvas (competitive alternatives, differentiated value, best-fit customer, category) plus a strategic narrative and sales-pitch storyboard, and grades existing positioning or messaging. Use for 'positioning', 'how do we describe our product', 'messaging', 'our pitch isn't landing', 'category', 'differentiation', 'one-liner', 'value prop', 'old game new game'. Draws on 43 Lenny's Podcast guests incl. April Dunford, Andy Raskin and Arielle Jackson.

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Work on the core package (types, validation, normalization, diff). Use when modifying DSL processing logic, adding new node/edge properties, changing validation rules, or updating the diff algorithm.

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Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.

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Adversarially review something just built — presume it is broken and find where. Use after implementing a feature, finishing a build, or before shipping, or whenever ATLAS or Boss wants a hostile second opinion on a diff, a running app, or a whole codebase. Spawns clean-context reviewers with opposing lenses (correctness, security, empty-world) and reproduces every finding by running the target before believing it. Distinct from /code-review, which statically reads a diff and never runs the app.

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Bulk RNA-seq DE with R/Bioconductor DESeq2. Negative binomial GLM, empirical Bayes shrinkage, Wald/LRT tests, multi-factor designs, Salmon tximeta import, apeglm LFC shrinkage, MA/volcano/heatmap viz. R gold standard. Use pydeseq2-differential-expression for Python; use edgeR for TMM normalization.

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Diffusion-based docking that predicts protein-ligand poses without a predefined site. Use for blind docking, when traditional docking fails, or exploring multiple binding modes. Pipeline: prep protein (PDB) and ligand (SMILES/SDF), run inference, analyze confidence-ranked poses.

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Python library for single-particle tracking (SPT) in video microscopy via the Crocker-Grier algorithm. Locate particles (fluorescent spots, colloids, vesicles, cells) per frame, link into trajectories, filter short tracks, and compute MSD for diffusion analysis. 2D/3D with subpixel accuracy; reads TIF stacks, AVI, image series via pims. Use for quantitative SPT and diffusion coefficient extraction from fluorescence or brightfield video.

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