Data analysis, machine learning, LLM apps, and prompt design (8.9K skills)
Core ML, Create ML, Vision framework, Natural Language framework, on-device ML integration. Use when user wants image classification, text analysis, object detection, sound classification, model optimization, or custom model integration. Covers Core ML vs Foundation Models decision.
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Generates protocol-based analytics infrastructure with swappable providers (TelemetryDeck, Firebase, Mixpanel). Use when user wants to add analytics, track events, or set up telemetry.
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On-device LLM integration using Apple's Foundation Models framework. Use when implementing AI text generation, structured output, or tool calling.
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When the user wants to create or optimize in-app paywalls, upgrade screens, upsell modals, or feature gates. Also use when the user mentions "paywall," "upgrade screen," "upgrade modal," "upsell," "feature gate," "convert free to paid," "freemium conversion," "trial expiration screen," "limit reached screen," "plan upgrade prompt," or "in-app pricing." Distinct from public pricing pages (see page-cro) — this skill focuses on in-product upgrade moments where the user has already experienced value.
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When the user wants help with revenue operations, lead lifecycle management, or marketing-to-sales handoff processes. Also use when the user mentions 'RevOps,' 'revenue operations,' 'lead scoring,' 'lead routing,' 'MQL,' 'SQL,' 'pipeline stages,' 'deal desk,' 'CRM automation,' 'marketing-to-sales handoff,' or 'data hygiene.' For cold outreach emails, see cold-email. For email drip campaigns, see email-sequence. For pricing decisions, see pricing-strategy.
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When the user wants to set up, improve, or audit analytics tracking and measurement. Also use when the user mentions "set up tracking," "GA4," "Google Analytics," "conversion tracking," "event tracking," "UTM parameters," "tag manager," "GTM," "analytics implementation," or "tracking plan." For A/B test measurement, see ab-test-setup.
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SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind mRNA. Ideally, unique molecular identifiers at a spot measure spot-specific expression, but this is often not the case due to bleed from nearby spots, an artifact we refer to as spot swapping. SpotClean is able to estimate the contamination rate in observed data and decontamin
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This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the 'sample by features' table of peak intensities in addition to the sample and feature metadata (as a single ExpressionSet object for subsequent statistical analysis). This package also permit usefull tools for cohorts management as analyzing data progressively, visualization tools and quality control. The steps include calibration, expiration detection, peak detection and qua
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omicsViewer visualizes ExpressionSet (or SummarizedExperiment) in an interactive way. The omicsViewer has a separate back- and front-end. In the back-end, users need to prepare an ExpressionSet that contains all the necessary information for the downstream data interpretation. Some extra requirements on the headers of phenotype data or feature data are imposed so that the provided information can be clearly recognized by the front-end, at the same time, keep a minimum modification on the existin
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The ORFhunteR package is a R and C++ library for an automatic determination and annotation of open reading frames (ORF) in a large set of RNA molecules. It efficiently implements the machine learning model based on vectorization of nucleotide sequences and the random forest classification algorithm. The ORFhunteR package consists of a set of functions written in the R language in conjunction with C++. The efficiency of the package was confirmed by the examples of the analysis of RNA molecules fr
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The package comprises a set of pretrained machine learning models to predict basic immune cell types. This enables all users to quickly get a first annotation of the cell types present in their dataset without requiring prior knowledge. scAnnotatR also allows users to train their own models to predict new cell types based on specific research needs.
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Image segmentation is the process of identifying the borders of individual objects (in this case cells) within an image. This allows for the features of cells such as marker expression and morphology to be extracted, stored and analysed. simpleSeg provides functionality for user friendly, watershed based segmentation on multiplexed cellular images in R based on the intensity of user specified protein marker channels. simpleSeg can also be used for the normalization of single cell data obtained f
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Implements low-level utilities for single-cell trajectory analysis, primarily intended for re-use inside higher-level packages. Include a function to create a cluster-level minimum spanning tree and data structures to hold pseudotime infere
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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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NanoTube includes functions for the processing, quality control, analysis, and visualization of NanoString nCounter data. Analysis functions include differential analysis and gene set analysis methods, as well as postprocessing steps to help understand the results. Additional functions are included to enable interoperability with other Bioconductor NanoString data analysis packages.
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Pathview is a stand-alone software package for pathway based data integration and visualization.
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The scDblFinder package gathers various methods for the detection and handling of doublets/multiplets in single-cell sequencing data (i.e. multiple cells captured within the same droplet or reaction volume). It includes methods formerly fou
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Variance-stabilizing transformations help with the analysis of heteroskedastic data (i.e., data where the variance is not constant, like count data). This package provide two types of variance stabilizing transformations: (1) methods based on the delta method (e.g., 'acosh', 'log(x+1)'), (2) model residual based (Pearson and randomized quantile residuals).
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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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Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.
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The package implements a method for normalising microarray intensities from single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of th
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'treeio' is an R package to make it easier to import and store phylogenetic tree with associated data; and to link external data from different sources to phylogeny. It also supports exporting phylogenetic tree with heterogeneous associated
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Defines an S4 class for storing data from spatial -omics experiments. The class extends SingleCellExperiment to support storage and retrieval of additional information from spot-based and molecule-based platforms, including spatial coordina
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A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control and visualization.
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