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概要と使いどころ
SpatialDE is a method to find spatially variable genes (SVG) from spatial transcriptomics data. This package provides wrappers to use the Python SpatialDE library in R, using reticulate and basilisk.
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SpatialFeatureExperiment (SFE) is a new S4 class for working with spatial single-cell genomics data. The voyager package implements basic exploratory spatial data analysis (ESDA) methods for SFE. Univariate methods include univariate global spatial ESDA methods such as Moran's I, permutation testing for Moran's I, and correlograms. Bivariate methods include Lee's L and cross variogram. Multivariate methods include MULTISPATI PCA and multivariate local Geary's C recently developed by Anselin. The
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Provides basic utility functions for performing single-cell analyses, focusing on simple normalization, quality control and data transformations. Also provides some helper functions to assist development of other packages.
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The epistack package main objective is the visualizations of stacks of genomic tracks (such as, but not restricted to, ChIP-seq, ATAC-seq, DNA methyation or genomic conservation data) centered at genomic regions of interest. epistack needs three different inputs: 1) a genomic score objects, such as ChIP-seq coverage or DNA methylation values, provided as a `GRanges` (easily obtained from `bigwig` or `bam` files). 2) a list of feature of interest, such as peaks or transcription start sites, provi
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Statistical and computational method to analyze the co-expression of gene pairs at single cell level. It provides the foundation for single-cell gene interactome analysis. The basic idea is studying the zero UMI counts' distribution instead of focusing on positive counts; this is done with a generalized contingency tables framework. COTAN can effectively assess the correlated or anti-correlated expression of gene pairs. It provides a numerical index related to the correlation and an approximate
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Seamlessly interfaces the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases. This work was partially supported by grant no. R21HG005912 from the National Human Genome Research Institute.
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This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limi
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Provides S4 data structures and basic functions to deal with flow cytometry data.
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The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R packag
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Microbiome time series simulation with generalized Lotka-Volterra model, Self-Organized Instability (SOI), and other models. Hubbell's Neutral model is used to determine the abundance matrix. The resulting abundance matrix is applied to (Tree)SummarizedExperiment objects.
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Some basic functions for filtering genes.
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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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Automatic code quality and best practices analysis. Use proactively when files are modified, saved, or committed. Analyzes code style, patterns, potential bugs, and security basics. Triggers on file changes, git diff, code edits, quality mentions.
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Run a basic E2E behavioral probe — one primary scenario smoke test for the grooming step.
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Helps the user come up with free lead magnets or hooks to offer in cold emails. Asks about their business, what they can legally give away, and what would be genuinely valuable to their ICP. Returns 5-10 concrete offer ideas with example CTA phrasings. Use when the user says their campaign "needs a hook", "needs an offer", "what can I give away", or when ICP onboarding flagged a missing lead magnet.
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Advanced full SEO audit skill. Runs its own full workflow from local scripts, including the basic SEO checks plus PageSpeed, social metadata, and advanced review modules when available.
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Full-spectrum Amazon competitor analysis. Compare listings, pricing, reviews, advertising strategy, and market positioning against direct competitors. Identify weaknesses to exploit and strengths to counter. Use when the user asks about competitor analysis, competitive research, ASIN comparison, pricing analysis, or how to beat competitors on Amazon.
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Amazon A+ Content strategy and creation. Module layouts, persuasive copy, comparison charts, image briefs, and conversion optimization. Use when the user asks about A+ Content, Enhanced Brand Content, product storytelling, or Amazon listing enhancement.
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Amazon competitor monitoring and competitive intelligence for sellers. Track pricing changes, inventory levels, new product launches, review velocity, and advertising patterns for competitor ASINs. Set up monitoring alerts for price drops, stock-outs, and market changes. Works on 12 Amazon marketplaces. No API key required. Use when: (1) monitoring competitor pricing strategies, (2) tracking competitor inventory and stock patterns, (3) detecting new product launches in your category, (4) analyzing competitor review velocity and ratings, (5) identifying market opportunities from competitor gaps, (6) setting up competitive alerts and benchmarks.
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Run a large-scale language migration with the six-step process: create the map and the rules, stress-test the rules, translate everything, compile, run it, match behavior. Use when the user wants to migrate, port, or rewrite a codebase from one language to another ("migrate this to Rust", "port our Python CLI to TypeScript", "should we rewrite this in Go?"), or asks for a migration feasibility assessment. Not for incremental JS→TS adoption — that needs no machinery — or single-file conversions.
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Review REST API contracts for HTTP semantics, versioning, backward compatibility, and response consistency. Use when user asks "review API", "check endpoints", "REST review", or before releasing API changes.
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Build a WhatsApp marketing strategy — WhatsApp Business setup, broadcast campaigns, automated flows, customer service, drip sequences, and conversational marketing. Use when the user says "WhatsApp marketing", "WhatsApp Business", "WhatsApp campaigns", "WhatsApp broadcasts", "WhatsApp automation", "WhatsApp drip", "market on WhatsApp", "WhatsApp for business", "WhatsApp chatbot", "WhatsApp customer service", "WhatsApp API", "messaging marketing India", or wants to use WhatsApp as a marketing and customer communication channel. Especially relevant for brands in India, the Middle East, Southeast Asia, Brazil, and Africa.
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Use when the user asks about Moodboard, building a moodboard from reference images, curated moodboard presets, Soul Hex color transfer, applying a visual style direction to generations, or named moodboard styles like Y2K studio, Warm ambient, Theatrical light, Swag era, Flash editorial, Street photography, Asian nostalgia, Retro BW, Surreal solarization, etc.
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Line-by-line copy editing and improvement for marketing content. Polish existing copy for clarity, conciseness, impact, and conversion. Trigger phrases: "edit my copy", "improve this copy", "polish this text", "copy edit", "make this clearer", "tighten this up", "proofread", "review my copy", "make this more persuasive", "fix my writing".
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