bioMate-AI

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Current version only works in 'merge' mode: A single table of gene summarizations is generated with one column for each sample file.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

SpatialFeatureExperiment (SFE) is a new S4 class for working with spatial single-cell genomics data. The voyager package implements basic exploratory spatial data analysis (ESDA) methods for SFE. Univariate methods include univariate global spatial ESDA methods such as Moran's I, permutation testing for Moran's I, and…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, En.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Annotate variants, compute amino acid coding changes, predict coding outcomes.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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.

bioMate-AI/biomate-connector

Skill Claude CodeCodex

Run real bioinformatics, drug-discovery, and clinical workflows on BioMate's BioMate cloud infrastructure. Use whenever the user asks to screen compounds (ADMET, docking), analyze sequencing data (RNA-seq, WGS, variant calling), reconstruct cryo-EM, model PK/PBPK, predict protein structure, or generate IND / CRO…