bioMate-AI/biomate-bioconductor-kb

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essenti.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Reactome is a free, open-source, curated and peer-reviewed pathway database. Their goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Tools for finding bumps in genomic data.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

ChIPseeker is a Bioconductor package for annotating ChIP-seq data analysis. Peak Annotation is performed by the annotatePeak function. The position and strand information of nearest genes are reported, in addition to the distance from the p.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Detect differential enrichment regions (peaks) across multiple experimental conditions and classify peaks into combinatorial patterns of enrichment.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

This package builds on existing tools and adds some simple but extremely useful capabilities for working wth ChIP-Seq data. The focus is on detecting differential binding windows/regions. One set of functions focusses on set-operations retaining mcols for GRanges objects, whilst another group of functions are to aid…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. The HiC-DC+ (Hi-C/HiChIP direct caller plus) package enables principled statistical analysis of Hi-C and HiChIP data sets – including calling significant interactions within a single experiment and performing differential analysis between…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

R generic interface to Hi-C contact matrices in .(m)cool, .hic or HiC-Pro derived formats, as well as other Hi-C processed file formats. Contact matrices can be partially parsed using a random access method, allowing a memory-efficient representation of Hi-C data in R. The HiCExperiment class stores the Hi-C contacts…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

The Model-based Analysis of ChIP-Seq (MACS) is a widely used toolkit for identifying transcript factor binding sites. This package is an R wrapper of the lastest MACS3.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Microbiome time series simulation with generalized Lotka-Volterra model, Self-Organized Instability (SOI), and other models. Hubbell's Neutral model is used to determine the abundance matrix. The resulting abundance matrix is applied to (Tree)SummarizedExperiment objects.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Tools to analyze & visualize Illumina Infinium methylation arrays.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Installs a self-contained conda instance that is managed by the R/Bioconductor installation machinery. This aims to provide a consistent Python environment that can be used reliably by Bioconductor packages. Functions are also provided to e.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Functions that are needed by many other packages or which replace R functions.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated me.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

The FDA Adverse Event Reporting System (FAERS) is a database used for the spontaneous reporting of adverse events and medication errors related to human drugs and therapeutic biological products. faers pacakge serves as the interface between the FAERS database and R. Furthermore, faers pacakge offers a standardized…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files. GDS is portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Some basic functions for filtering genes.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Functions for plotting genomic data.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Graph objects from pathway topology derived from KEGG, Panther, PathBank, PharmGKB, Reactome SMPDB and WikiPathways databases.