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概要と使いどころ
MetaboCoreUtils defines metabolomics-related core functionality provided as low-level functions to allow a data structure-independent usage across various R packages. This includes functions to calculate between ion (adduct) and compound ma
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Data quality assessment is an integral part of preparatory data analysis to ensure sound biological information retrieval. We present here the MatrixQCvis package, which provides shiny-based interactive visualization of data quality metrics at the per-sample and per-feature level. It is broadly applicable to quantitative omics data types that come in matrix-like format (features x samples). It enables the detection of low-quality samples, drifts, outliers and batch effects in data sets. Visualiz
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tags: [bioconductor, r, proteomics, vignette-grounded]
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The PSMatch package helps proteomics practitioners to load, handle and manage Peptide Spectrum Matches. It provides functions to model peptide-protein relations as adjacency matrices and connected components, visualise these as graphs and m
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Save MultiAssayExperiments to h5mu files supported by muon and mudata. Muon is a Python framework for multimodal omics data analysis. It uses an HDF5-based format for data storage.
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A first step in the data analysis of Mass Spectrometry (MS) based proteomics data is to identify peptides and proteins. With this respect the huge number of experimental mass spectra typically have to be assigned to theoretical peptides derived from a sequence database. Search engines are used for this purpose. These tools compare each of the observed spectra to all candidate theoretical spectra derived from the sequence data base and calculate a score for each comparison. The observed spectrum
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MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.
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cogeqc aims to facilitate systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable parameters for each data set. cogeqc can be used to asses: i. genome assembly and annotation quality with BUSCOs and comparisons of statistics with publicly available genomes on the NCBI; ii. orthogroup inference using a protein domain-based approach and; iii. synteny detection using synteny network properties. There are also data visualizat
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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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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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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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Evaluate and plan Amazon marketplace expansion across countries and regions. Use when a seller asks which Amazon marketplace to enter, how to compare international demand and economics, what tax, product-compliance, logistics, localization, account, or launch workstreams to investigate, or how to build a gated global-selling roadmap. Do not use as legal, tax, customs, or certification advice.
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Deep learning for single-cell analysis using scvi-tools. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq multi-modal analysis with totalVI, (4) multiome RNA+ATAC analysis with MultiVI, (5) spatial transcriptomics deconvolution with DestVI, (6) label transfer and reference mapping with scANVI/scArches, (7) RNA velocity with veloVI, or (8) any deep learning-based single-cell method. Triggers include mentions of scVI, scANVI, totalVI, PeakVI, MultiVI, DestVI, veloVI, sysVI, scArches, variational autoencoder, VAE, batch correction, data integration, multi-modal, CITE-seq, multiome, reference mapping, latent space.
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Naming conventions, API ergonomics, and usability patterns for functional code
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Use when customers should bring other customers — one-way versus two-way incentives, reward structure and economics, trigger moments, referral messaging, tracking and attribution, fraud controls, and anti-spam compliance by region: TCPA for US, GDPR for EU, PDPA for SEA, LGPD for LATAM. Trigger on 'referral program', 'refer a friend', 'word of mouth', 'viral loop', 'how do I get customers to bring friends', 'affiliate rewards'. Also use when the user has happy customers and no system to use them. Not for — running your own community space, see `28-community-building-global`; posting inside third-party communities, see `38-community-seeding-global`; email flow mechanics, see `14-email-marketing-global`.
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Knowledge comic creator supporting multiple art styles and tones. Creates original educational comics with detailed panel layouts and sequential image generation. Use when user asks to create "知识漫画", "教育漫画", "biography comic", "tutorial comic", or "Logicomix-style comic".
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Evaluates new product opportunities through demand, channels and economics before committing to build.
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Identify error-prone APIs, dangerous configuration, and footgun designs that enable security mistakes. Use for API ergonomics, misuse resistance, secure defaults, or pit-of-success reviews; use code-review for general defects.
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Use when you need framework-agnostic Docker and container image guidance for Java projects - Dockerfile design, multi-stage Maven builds, jlink custom runtimes, micro runtime distributions such as Alpaquita, JVM container ergonomics, non-root execution, image metadata, .dockerignore, reproducible builds, vulnerability scanning, SBOM awareness, and production-safe container defaults. This should trigger for requests such as Review Java Dockerfile; Improve Docker image security; Add jlink runtime to a Java container; Add containerization to a Java project; Optimize Java container image size; Review Docker build reproducibility. Part of Plinth Toolkit
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This skill should be used when building a personal productivity or operating system for a CEO, founder, or executive. Triggers on "personal OS", "annual review", "life planning", "goal setting system", "Bill Campbell", "Trillion Dollar Coach", "startup failure patterns", "Good to Great", "Level 5 Leadership", "Buy Back Your Time", "E-Myth", "Customer Development", "Steve Blank", "Small Is Beautiful", "Schumacher", "human-scale", "subsidiarity", "Buddhist economics", "permanence".
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Character consistency across AI-generated images with reference sheets and LoRA techniques. Covers turnaround views, expression sheets, color palettes, and style consistency tricks. Use for: character design, game art, illustration, animation, comics, visual novels. Triggers: character design, character sheet, character consistency, character reference, turnaround sheet, expression sheet, character art, consistent character, character concept, reference sheet, character creation, oc design, character bible
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Token supply dynamics, vesting analysis, inflation modeling, and valuation frameworks for crypto tokens
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High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.
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Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.
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