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This is an advanced version of TDbasedUFE, which is a comprehensive package to perform Tensor decomposition based unsupervised feature extraction. In contrast to TDbasedUFE which can perform simple the feature selection and the multiomics analyses, this package can perform more complicated and advanced features, but they are not so popularly required. Only users who require more specific features can make use of its functionality.

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This package enables the interpretation and analysis of results from a gene set enrichment analysis using network-based and text-mining approaches. Most enrichment analyses result in large lists of significant gene sets that are difficult to interpret. Tools in this package help build a similarity-based network of significant gene sets from a gene set enrichment analysis that can then be investigated for their biological function using text-mining approaches.

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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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Zenith performs gene set analysis on the result of differential expression using linear (mixed) modeling with dream by considering the correlation between gene expression traits. This package implements the camera method from the limma package proposed by Wu and Smyth (2012). Zenith is a simple extension of camera to be compatible with linear mixed models implemented in variancePartition::dream().

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This package encapsulate many functions to conduct a differential topology analysis. It focuses on analyzing an 'omic dataset with multiple conditions. While the package is mostly geared toward scRNASeq, it does not place any restriction on the actual input format.

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This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the option to create or extend a reference atlas and,also simulate the desired size of the bulk signature profile of the reference cell types.The package includes the cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can be used in deconvolution. Additionally,we included BS

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granulator is an R package for the cell type deconvolution of heterogeneous tissues based on bulk RNA-seq data or single cell RNA-seq expression profiles. The package provides a unified testing interface to rapidly run and benchmark multiple state-of-the-art deconvolution methods. Data for the deconvolution of peripheral blood mononuclear cells (PBMCs) into individual immune cell types is provided as well.

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This package provides the visualization of bayesian network inferred from gene expression data. The networks are based on enrichment analysis results inferred from packages including clusterProfiler and ReactomePA. The networks between pathways and genes inside the pathways can be inferred and visualized.

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This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data. The pipeline takes as input transcriptional and/or metabolic data and finds a metabolic subnetwork (module) most regulated between the two conditions of interest. The package further provides functions for module post-processing, annotation and visualization.

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This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, an

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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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the R package BioNAR, developed to step by step analysis of PPI network. The aim is to quantify and rank each protein’s simultaneous impact into multiple complexes based on network topology and clustering. Package also enables estimating of co-occurrence of diseases across the network and specific clusters pointing towards shared/common mechanisms.

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A package for demultiplexing single-cell sequencing experiments of pooled cells labeled with barcode oligonucleotides. The package implements methods to fit regression mixture models for a probabilistic classification of cells, including multiplet detection. Demultiplexing error rates can be estimated, and methods for quality control are provided.

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Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited. This package calls and reports cytosine methylation as well as frequencies of hypermethylated epialleles at the level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map (BAM) files as an input. Among other things, this package can also extract and visualise methylation patterns and assess allele specificity of methylation.

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The 'enrichplot' package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analysis. It is mainly designed to work with the 'clusterProfiler' package suite. All the visualizati

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The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and enc

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Analyze Java project architecture at macro level - package structure, module boundaries, dependency direction, and layering. Use when user asks "review architecture", "check structure", "package organization", or when evaluating if a codebase follows clean architecture principles.

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Design exclusive bonus packages that make YOUR affiliate link the obvious choice. Triggers on: "create bonuses for", "bonus stack", "what bonuses should I offer", "bonus ideas for", "exclusive bonuses", "differentiate my affiliate link", "why buy through my link", "affiliate bonuses", "bonus package", "what can I offer as a bonus", "design bonuses", "build a bonus stack".

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Package an existing talking-head / interview / podcast video with timed, designed GRAPHIC OVERLAY cards — kinetic titles, lower-thirds, data callouts, quotes, side panels, picture-in-picture — synced to the transcript, on a 16:9 / 9:16 / 4:5 canvas of your choice; the clip plays untouched underneath. Trigger on "graphic overlays", "on-screen graphics", "package / dress up my video". Not plain subtitles (/embedded-captions). Unclear → /hyperframes.

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Use when the user asks to create, scaffold, update or package a skill, or asks how skill frontmatter, progressive disclosure or bundled resources should be structured. Walks through init_skill.py, writing SKILL.md and package_skill.py.

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Maintain package-level `agentmap.md` files as outline-level maps of the real file tree and core responsibilities. Use when package structure or responsibility boundaries change and the corresponding `agentmap.md` must be created or updated.

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Structure Go code with package-first boundaries, `cmd/` and `internal/`, and explicit dependency wiring. Use when shaping project layout, package ownership, or service boundaries in Go; defer Redis/cache-specific implementation recipes to database skills.

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Create a release checklist and GitHub issue for an R package. Use when the user asks to "create a release checklist" or "start a release" for an R package.

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Generate and improve accessible alt text for data visualizations and images in R packages and Quarto documents. Use when the user wants to add, improve, or audit alt text for figures in a pkgdown site or .qmd files. Activate for requests that mention fig-alt, fig.alt, figure descriptions, or alt text in the context of an R package or Quarto document.

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