The Model-based Analysis of ChIP-Seq (MACS) is a widely used toolkit for identifying transcript factor binding sites. This package is an R wrapper of the lastest MACS3.
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The Model-based Analysis of ChIP-Seq (MACS) is a widely used toolkit for identifying transcript factor binding sites. This package is an R wrapper of the lastest MACS3.
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ChIPseeker is a Bioconductor package for annotating ChIP-seq data analysis. Peak Annotation is performed by the annotatePeak function. The position and strand information of nearest genes are reported, in addition to the distance from the p
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The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor
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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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Infrastructure to support 'views' used to classify Bioconductor packages. 'biocViews' are directed acyclic graphs of terms from a controlled vocabulary. There are three major classifications, corresponding to 'software', 'annotation', and '
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Functions that are needed by many other packages or which replace R functions.
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This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local FDR values. The q-value of a test measures the proportion of false positives incurred (called the false
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Client for the gypsum REST API (https://gypsum.artifactdb.com), a cloud-based file store in the ArtifactDB ecosystem. This package provides functions for uploads, downloads, and various adminstrative and management tasks. Check out the docu
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The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose
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This package is a implementation of biclustering ensemble method MoSBi (Molecular signature Identification from Biclustering). MoSBi provides standardized interfaces for biclustering results and can combine their results with a multi-algorithm ensemble approach to compute robust ensemble biclusters on molecular omics data. This is done by computing similarity networks of biclusters and filtering for overlaps using a custom error model. After that, the louvain modularity it used to extract biclus
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基于 TrailSnap(行影集)现有设计系统设计、实现和审查前端 UI。适用于 package/website 的新页面、组件、布局、主题、移动端适配与界面改版;纯后端任务和其他项目不适用。
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Universal LaTeX document skill: create, compile, and convert any document to professional PDF with PNG previews. Supports resumes, reports, cover letters, invoices, academic papers, theses/dissertations, academic CVs, presentations (Beamer), scientific posters, formal letters, exams/quizzes, books, cheat sheets, reference cards, exam formula sheets, fillable PDF forms (hyperref form fields), conditional content (etoolbox toggles), mail merge from CSV/JSON (Jinja2 templates), version diffing (latexdiff), charts (pgfplots + matplotlib), tables (booktabs + CSV import), images (TikZ), Mermaid diagrams, AI-generated images, watermarks, landscape pages, bibliography/citations (BibTeX/biblatex), multi-language/CJK (auto XeLaTeX), algorithms/pseudocode, colored boxes (tcolorbox), SI units (siunitx), Pandoc format conversion (Markdown/DOCX/HTML ↔ LaTeX), and PDF-to-LaTeX conversion of handwritten or printed documents (math, business, legal, general). Compile script supports pdflatex, xelatex, lualatex with auto-detection, latexmk backend, texfot log filtering, PDF/A output, and verbosity control (--verbose/--quiet). Empirically optimized scaling: single agent 1-10 pages, split 11-20, batch-7 pipeline 21+. Use when user asks to: (1) create a resume/CV/cover letter, (2) write a LaTeX document, (3) create PDF with tables/charts/images, (4) compile a .tex file, (5) make a report/invoice/presentation, (6) anything involving LaTeX or pdflatex, (7) convert/OCR a PDF to LaTeX, (8) convert handwritten notes, (9) create charts/graphs/diagrams, (10) create slides, (11) write a thesis or dissertation, (12) create an academic CV, (13) create a poster, (14) create an exam/quiz, (15) create a book, (16) convert between document formats (Markdown, DOCX, HTML to/from LaTeX), (17) generate Mermaid diagrams for LaTeX, (18) create a formal business letter, (19) create a cheat sheet or reference card, (20) create an exam formula sheet or crib sheet, (21) condense lecture notes/PDFs into a cheat sheet, (22) create a fillable PDF form with text fields/checkboxes/dropdowns, (23) create a document with conditional content/toggles (show/hide sections), (24) generate batch/mail-merge documents from CSV/JSON data, (25) create a version diff PDF (latexdiff) highlighting changes between documents, (26) create a homework or assignment submission with problems and solutions, (27) create a lab report with data tables, graphs, and error analysis, (28) encrypt or password-protect a PDF, (29) merge multiple PDFs into one, (30) optimize/compress a PDF for web or email, (31) lint or check a LaTeX document for common issues, (32) count words in a LaTeX document, (33) analyze document statistics (figures, tables, citations), (34) fetch BibTeX from a DOI, (35) convert a Graphviz .dot file to PDF/PNG, (36) convert a PlantUML .puml file to PDF/PNG, (37) create a one-pager/fact sheet/executive summary, (38) create a datasheet or product specification sheet, (39) extract pages from a PDF (page ranges, odd/even), (40) check LaTeX package availability before compiling, (41) analyze citations and cross-reference with .bib files, (42) debug LaTeX compilation errors, (43) make a document accessible (PDF/A, tagged PDF), (44) create lecture notes or course handouts, (45) fill an existing PDF form (fillable fields or non-fillable with annotations), (46) extract text or tables from a PDF (pdfplumber, pypdf), (47) OCR a scanned PDF to text (pytesseract), (48) create a PDF programmatically with reportlab (Canvas, Platypus), (49) rotate or crop PDF pages (pypdf), (50) add a watermark to an existing PDF, (51) extract metadata from a PDF (title, author, subject).
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Check dependencies for known vulnerabilities using npm audit, pip-audit, etc. Use when package.json or requirements.txt changes, or before deployments. Alerts on vulnerable dependencies. Triggers on dependency file changes, deployment prep, security mentions.
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Expert knowledge for Azure Network Watcher development including troubleshooting, decision making, limits & quotas, security, configuration, and integrations & coding patterns. Use when configuring VNet/NSG flow logs, Traffic Analytics, packet capture, Connection Monitor migration, or VPN monitoring, and other Azure Network Watcher related development tasks. Not for Azure Monitor (use azure-monitor), Azure Virtual Network (use azure-virtual-network), Azure Networking (use azure-networking), Azure Firewall (use azure-firewall).
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Expert knowledge for Azure Artifacts development including best practices, decision making, limits & quotas, security, configuration, integrations & coding patterns, and deployment. Use when managing feeds, upstream sources, .npmrc auth, GitHub Actions CI/CD, or package retention limits, and other Azure Artifacts related development tasks. Not for Azure DevOps (use azure-devops), Azure Pipelines (use azure-pipelines), Azure Repos (use azure-repos), Azure Boards (use azure-boards).
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Use RightStack as a read-only Web3 stack advisor for architecture recommendations, workflow inspection, tool comparisons, and package-migration checks. Use for planning; do not treat corpus output as implementation proof.
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Bootstrap project-specific Trellis coding specs with a platform-neutral single-agent workflow. Use when creating or refreshing .trellis/spec guidelines, analyzing a codebase with GitNexus, ABCoder, or source inspection, decomposing package/layer spec work, and writing real codebase-backed spec docs without placeholder text.
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Product bundling strategy — virtual bundles, multi-pack pricing, cross-sell bundles, bundle listing optimization
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Plan shoot-ready Amazon product photography, listing image sets, infographics, lifestyle scenes, and production briefs. Use when a seller asks for an Amazon photo shot list, creative direction, image-pack plan, photography budget, DIY-versus-done-for-you decision, or handoff to a photographer or image-generation workflow. Do not use for listing copy or image-only performance auditing.
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Return rate reduction — root cause analysis, listing accuracy, packaging improvements, size guides
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Decide whether to add, keep, or remove a dependency. Use before adding any package.
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Turn a completed task, browser flow, artifact pipeline, failure-recovery trace, or repeatedly refined workflow into a new reusable skill package or a reviewed skill-design plan. Use when the user asks to make a new skill from real run history, extract a reusable workflow from conversation/logs/files, summarize lessons into a new skill, or produce a plan before writing files. Do not use to upgrade an existing skill or to execute the business workflow itself.
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Designs irresistible Grand Slam Offers using Alex Hormozi's value equation, obstacle-solution mapping, value-cost trim/stack, and offer-naming patterns. Use when fixing low conversion rates, packaging products, pricing services, designing high-converting offers, or when prospects browse but don't buy. Covers value stacking, guarantees, scarcity, urgency, and pricing psychology for validated markets.
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Use when the user mentions the Higgsfield CLI (binaries `higgsfield` / `higgs` / `hf`, `higgsfield auth login`, `higgsfield generate create`, `higgsfield workflow`, the `@higgsfield/cli` npm package), the Higgsfield MCP custom connector (`mcp.higgsfield.ai/mcp`) or its bundled workflows (`get_workflow_instructions` — character-sheet, thumbnail-generation, ugc-* videos, faceless-video, narrator, subtitles, product-photoshoot, brand-asset-creation, ad-multiplier, video-editing / Higgsedit, website-builder-flow), Higgsfield's bundled skills repo (`higgsfield-ai/skills` — `higgsfield-generate`, `higgsfield-soul-id`, `higgsfield-product-photoshoot`, `higgsfield-brandkit`, `higgsfield-marketplace-cards`, `higgsfield-websites`, `higgsfield-video-explainer`, `higgsfield-youtube-thumbnail`, invoked as `/higgsfield:generate` etc.), or asks how this skill coexists with those tools (`do I need both`, `how does this work with the CLI/MCP/skills`, `should Higgsfield's workflow do this or you`).
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