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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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A robust and outlier-aware method for testing differential tissue composition from single-cell data. This model can infer changes in tissue composition and heterogeneity, and can produce realistic data simulations based on any existing dataset. This model can also transfer knowledge from a large set of integrated datasets to increase accuracy further.

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Precise knowledge on the binding sites of an RNA-binding protein (RBP) is key to understand (post-) transcriptional regulatory processes. Here we present a workflow that describes how exact binding sites can be defined from iCLIP data. The package provides functions for binding site definition and result visualization. For details please see the vignette.

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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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Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including

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Provides R wrappers of several on-target and off-target scoring methods for CRISPR guide RNAs (gRNAs). The following nucleases are supported: SpCas9, AsCas12a, enAsCas12a, and RfxCas13d (CasRx). The available on-target cutting efficiency scoring methods are RuleSet1, Azimuth, DeepHF, DeepCpf1, enPAM+GB, and CRISPRscan. Both the CFD and MIT scoring methods are available for off-target specificity prediction. The package also provides a Lindel-derived score to predict the probability of a gRNA to

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Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA) provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP and Copy number variation data. It's easy to download data from TCGA using the gdc tool, but processing these data into a format suitable for bioinformatics analysis requires more work. This R package was developed to handle these data.

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ASURAT is a software for single-cell data analysis. Using ASURAT, one can simultaneously perform unsupervised clustering and biological interpretation in terms of cell type, disease, biological process, and signaling pathway activity. Inputting a single-cell RNA-seq data and knowledge-based databases, such as Cell Ontology, Gene Ontology, KEGG, etc., ASURAT transforms gene expression tables into original multivariate tables, termed sign-by-sample matrices (SSMs).

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Provides functionalities to visualize and contextualize CRISPR guide RNAs (gRNAs) on genomic tracks across nucleases and applications. Works in conjunction with the crisprBase and crisprDesign Bioconductor packages. Plots are produced using the Gviz framework.

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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 parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less 'pretty' output than a vendor specific parser. Please contact th

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MEM, Marker Enrichment Modeling, automatically generates and displays quantitative labels for cell populations that have been identified from single-cell data. The input for MEM is a dataset that has pre-clustered or pre-gated populations with cells in rows and features in columns. Labels convey a list of measured features and the features' levels of relative enrichment on each population. MEM can be applied to a wide variety of data types and can compare between MEM labels from flow cytometry,

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This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local FDR values. The q-value of a test measures the proportion of false positives incurred (called the false

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This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enric

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In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. bio

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Expert knowledge for Azure Quotas development including limits & quotas. Use when requesting per-region Storage account quota increases, checking limits, or filing Azure support requests, and other Azure Quotas related development tasks. Not for Azure Cost Management (use azure-cost-management), Azure Monitor (use azure-monitor), Azure Policy (use azure-policy), Azure Resource Manager (use azure-resource-manager).

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Expert knowledge for Azure Spring Apps development including troubleshooting, best practices, decision making, architecture & design patterns, limits & quotas, security, configuration, integrations & coding patterns, and deployment. Use when configuring ASA networking/security, Tanzu tools, observability/APM, CI/CD deployments, or blue‑green releases, and other Azure Spring Apps related development tasks. Not for Azure App Service (use azure-app-service), Azure Container Apps (use azure-container-apps), Azure Kubernetes Service (AKS) (use azure-kubernetes-service), Azure Functions (use azure-functions).

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Expert knowledge for Azure External Attack Surface Management development including configuration. Use when filtering EASM inventory by ASN, domains, hosts, IPs, pages, SSL certs, or exporting findings to analytics tools, and other Azure External Attack Surface Management related development tasks. Not for Azure Defender For Cloud (use azure-defender-for-cloud), Azure Security (use azure-security), Azure Sentinel (use azure-sentinel), Azure Networking (use azure-networking).

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Expert guidance for designing Azure solutions using Azure Architecture. Covers reference architectures, solution ideas, design patterns, technology choices, architecture styles, best practices, anti-patterns, example workloads, and migration guides. Use when designing AKS/microservices, hybrid/Arc, SAP or mainframe migrations, IoT/Edge, or mission-critical BCDR, and other Azure Architecture related development tasks.

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Create new skills, modify and improve existing skills, and measure skill performance. Use when users want to create a skill from scratch, edit, or optimize an existing skill, run evals to test a skill, benchmark skill performance with variance analysis, or optimize a skill's description for better triggering accuracy.

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Build crafted, highly detailed, interactive isometric SVG figures that explain a technical idea as a real physical object (a test rig, a dial gauge, a cabinet of drawers, a plotter, a lock), with many small precise solid parts, four-tone shading, correct painter's order, a framed card with title, hint and live readout, and calm eased motion. Use this whenever someone wants an isometric illustration, an explanatory diagram or figure for docs, a blog post, a landing page or an article, a "Linear-style" or "premium" technical drawing, an interactive explainer, or an SVG that shows how a system, algorithm or component works, even if they never say "isometric". Works framework-free (TypeScript/JS that writes SVG and HTML) and in React/Next.js, and can add realistic WebGL shaders (fire, exhaust, water, caustics, lamp light) that live inside the drawing in the same isometric perspective.

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Three-mode idea engine - generate collides the week's zeitgeist with what you can ship into scored wedges; validate viability-screens the idea backlog; memo writes evidence-backed startup memos.

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Execution-gap audit - cross-references the startup idea backlog against shipped skills, prototypes, and cross-repo PRs, surfacing the top 3 ideas to build next by narrative and operator fit.

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Generates 15-25+ cold outbound campaign ideas with targeting strategies, AI personalization approaches, and value propositions. Use when planning campaign experiments for a client, given their website or business context.

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