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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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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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The 'msa' package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any externa

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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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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 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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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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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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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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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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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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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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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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Set up and run an Aeon agent instance - get started from scratch, pick which skills to turn on or install more from packs, reschedule or change what runs, edit what an existing skill does, fix a skill that isn't firing, set the STRATEGY.md north star and soul/ voice, turn a coding-agent chat into a scheduled Aeon skill, and mine past coding-agent conversations for recurring work worth automating as a skill. Use when the user mentions Aeon, aeon.yml, an Aeon skill / instance / routine / pack, asks to schedule, enable, edit, or debug an agent that runs on a cron, or asks what of their repeated/manual work Aeon could take over.

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Install a community skill pack into this fork from a GitHub repo and ship it as an auto-merged PR

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Discovers and injects project-specific coding guidelines from .trellis/spec/ before implementation begins. Reads spec indexes, pre-development checklists, and shared thinking guides for the target package. Use when starting a new coding task, before writing any code, switching to a different package, or needing to refresh project conventions and standards.

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Build a product-specific Amazon FBA prep, labeling, packing, and shipment-readiness plan. Use when a seller asks how to prepare units for FBA, choose barcode and labeling steps, plan poly-bagging, bubble wrap, sets, case packs, cartons, dangerous-goods review, supplier or prep-center instructions, or prevent receiving delays. Do not use as a substitute for current Seller Central requirements.

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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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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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Weekdays. Works the next ready card on the board, one card per run, and assembles what it needs as a complete local file ready to paste: a campaign build sheet, a negative keyword file, a conversion action specification, an audience definition, or an upload packet. The whole step happens in a text editor until you release the ad account in RELEASES.md, and then Step 6a publishes the approved package through a connection you already have and writes a receipt for every id the platform returns.

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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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