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概要と使いどころ
Installs a self-contained conda instance that is managed by the R/Bioconductor installation machinery. This aims to provide a consistent Python environment that can be used reliably by Bioconductor packages. Functions are also provided to e
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R generic interface to Hi-C contact matrices in `.(m)cool`, `.hic` or HiC-Pro derived formats, as well as other Hi-C processed file formats. Contact matrices can be partially parsed using a random access method, allowing a memory-efficient representation of Hi-C data in R. The `HiCExperiment` class stores the Hi-C contacts parsed from local contact matrix files. `HiCExperiment` instances can be further investigated in R using the `HiContacts` analysis package.
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This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated me
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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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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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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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Infrastructure shared by all the Biostrings-based genome data packages.
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This package supports functional characteristics of both coding and non-coding genomics data for thousands of species with up-to-date gene annotation. It provides a univeral interface for gene functional annotation from a variety of sources
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Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various
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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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This package builds on existing tools and adds some simple but extremely useful capabilities for working wth ChIP-Seq data. The focus is on detecting differential binding windows/regions. One set of functions focusses on set-operations retaining mcols for GRanges objects, whilst another group of functions are to aid visualisation of results. Coercion to tibble objects is also implemented.
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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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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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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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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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Package one of this agent's own skills as a standalone community pack and submit it to the aeon registry as a PR
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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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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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Evaluate whether a Stripe dispute is economical to contest, then gather evidence and submit only when approved. Use for Stripe disputes, chargebacks, counter-disputes, evidence packages, or Stripe dispute IDs.
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