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概要と使いどころ
mirTarRnaSeq R package can be used for interactive mRNA miRNA sequencing statistical analysis. This package utilizes expression or differential expression mRNA and miRNA sequencing results and performs interactive correlation and various GLMs (Regular GLM, Multivariate GLM, and Interaction GLMs ) analysis between mRNA and miRNA expriments. These experiments can be time point experiments, and or condition expriments.
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The MsDataHub package uses the ExperimentHub infrastructure to distribute raw mass spectrometry data files, peptide spectrum matches or quantitative data from proteomics and metabolomics experiments.
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This R package supports interactive visualization of multi-channel images and segmentation masks generated by imaging mass cytometry and other highly multiplexed imaging techniques using shiny. The cytoviewer interface is divided into image-level (Composite and Channels) and cell-level visualization (Masks). It allows users to overlay individual images with segmentation masks, integrates well with SingleCellExperiment and SpatialExperiment objects for metadata visualization and supports image do
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Defines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metada
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The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data. Experimental methods supported include dynamic LOPIT-DC, hyperLOPIT, Dynamic Organellar Maps, Dynamic PCP. It provides Bioconductor infrastructure to analyse these data.
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Build a growth strategy with frameworks, metrics, and experimentation. Use when the user says "growth strategy", "growth plan", "AARRR", "growth loops", "North Star Metric", "growth model", "activation rate", "retention strategy", "churn reduction", "growth experiments", or asks about overall growth frameworks and metrics for their product.
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Plan, triage, and write academic rebuttals and review responses. Use when an AI research agent needs to handle conference, journal, workshop, or grant reviews; classify reviewer concerns; decide what evidence or experiments can change the decision; write an AC-facing executive summary; draft per-reviewer responses; correct factual misunderstandings without sounding hostile; handle novelty, baseline, method, experiment, clarity, and scope objections; or produce a final rebuttal checklist.
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Review and revise academic papers with a senior-reviewer workflow. Use when an AI research/coding agent needs to work on an existing paper draft, PDF, LaTeX project, Word document, markdown manuscript, rejected paper, or paper idea that already has a concrete direction, and produce: paper maps, weakness audits, insight/novelty checks, reviewer objections, claim-experiment matrices, theory/proof checks, experiment plans, statistics/reproducibility audits, figure/table audits, ethics/compliance checks, revision plans, detailed section edits, or final submission checklists.
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Step 2 of the PaperOrchestra pipeline (arXiv:2604.05018). Execute the visualization plan from outline.json — render plots and conceptual diagrams from experimental_log.md and idea.md, optionally refine via VLM critique loop, and produce context-aware captions. Runs in parallel with the literature-review-agent. TRIGGER when the orchestrator delegates Step 2 or when the user asks to "generate the figures for my paper" or "render the plots from this experiment log".
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Orchestrate the full PaperOrchestra (Song et al., 2026, arXiv:2604.05018) five-agent pipeline to turn unstructured research materials (idea, experimental log, LaTeX template, conference guidelines, optional figures) into a submission-ready LaTeX manuscript and compiled PDF. TRIGGER when the user asks to "write a paper from my experiments", "turn this idea and these results into a paper", "generate a conference submission", "run paper-orchestra on X", or otherwise wants the end-to-end paper-writing pipeline. Coordinates the outline-agent, plotting-agent, literature-review-agent, section-writing-agent, and content-refinement-agent skills.
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Guidance for managing R package lifecycle according to tidyverse principles using the lifecycle package. Use when: (1) Setting up lifecycle infrastructure in a package, (2) Deprecating functions or arguments, (3) Renaming functions or arguments, (4) Superseding functions, (5) Marking functions as experimental, (6) Understanding lifecycle stages (stable, experimental, deprecated, superseded), or (7) Writing deprecation helpers for complex scenarios.
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Archived DESIGN.md impact experiment compatibility gate. Use when an old Lab #01 run is requested, but do not generate new legacy 9/12-section documents; direct new experiments to the Core v2 benchmark track.
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Strategic guidance for operationalizing machine learning models from experimentation to production. Covers experiment tracking (MLflow, Weights & Biases), model registry and versioning, feature stores (Feast, Tecton), model serving patterns (Seldon, KServe, BentoML), ML pipeline orchestration (Kubeflow, Airflow), and model monitoring (drift detection, observability). Use when designing ML infrastructure, selecting MLOps platforms, implementing continuous training pipelines, or establishing model governance.
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Use F# Interactive (`dotnet fsi`) for .NET exploration, scriptable experiments, package-backed .fsx workflows, quick data transforms, and reproducible command-line probes. USE FOR: .fsx scripts, F# REPL work, #r nuget references, #load composition, interactive type exploration, and small strongly typed experiments before moving code into a project. DO NOT USE FOR: production application code that needs compiled project structure; C# scripting; long-lived automation better expressed as a normal CLI, test, or build target. INVOKES: run dotnet fsi, edit .fsx scripts, load project or source files, and validate snippets against the target SDK.
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Execute one bounded RED to GREEN experiment from bead or caller intent; return derived subject identity and check facts. Triggers: "implement", "implement this bead", "run the experiment". Full plan-to-validation requests route to rpi.
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Summarize, organize, and normalize messy research materials into an IEEE-ready writing brief before manuscript drafting. Use when Codex needs to process a folder or collection of experiment logs, code files, AI chat exports, idea notes, literature summaries, related-work notes, copied introduction excerpts, Zotero-derived paper summaries, tables, figures, or scattered Markdown/text records and convert them into structured inputs for ieee-writing, ieee-experiment, ieee-citation, ieee-reviewer, or ieee-response.
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When the user wants to plan, design, or implement an A/B test or experiment, or build a growth experimentation program.
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Best practices for designing reproducible experiments
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Use when the user has a research question and needs a complete experiment package — design document, runnable code, results (measured or simulated with honest provenance), publication-grade figures, structured report. Single-stage, no Python runtime.
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End-to-end CRISPR experiment design from target selection to delivery-ready constructs. Covers guide RNA design, off-target assessment, and specialized editing strategies including knockouts, base editing, and HDR knockins. Use when designing complete CRISPR editing experiments for gene knockout, correction, or tagging.
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Query RCSB PDB for experimental protein structures. Use when user asks about crystal structures, X-ray, cryo-EM, NMR structures, or PDB IDs. Triggers on "pdb", "crystal structure", "cryo-em", "x-ray structure", "protein crystal", "experimental structure".
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Guidance for SPR and BLI binding characterization experiments. Use when: (1) Planning binding kinetics experiments, (2) Troubleshooting poor/no binding signal, (3) Interpreting kinetic data artifacts, (4) Choosing between SPR vs BLI platforms.
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Data Version Control for ML projects. Track large datasets and models alongside Git, build reproducible ML pipelines, and run experiments with metric comparison. Works with any storage backend including S3, GCS, Azure, and local filesystems.
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Build AI agents that automate scientific research — hypothesis generation, experiment design, data analysis, and paper writing using agentic tree search. Use when: automating research workflows, generating and testing hypotheses, building AI-powered research assistants.
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