bioMate-AI/biomate-bioconductor-kb

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

InterCellar is implemented as an R/Bioconductor Package containing a Shiny app that allows users to interactively analyze cell-cell communication from scRNA-seq data. Starting from precomputed ligand-receptor interactions, InterCellar provides filtering options, annotations and multiple visualizations to explore…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Given a matrix of counts (e.g. from featureCounts) and optional information about the genes, this tool performs differential expression (DE) using the limma Bioconductor package and produces plots and tables useful in DE analysis. Interacti.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Methods and models for handling zero-inflated single cell assay data.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Generate and refine a group-specific gene signature from a single transcriptomics dataset, including background tissue expression removal and visualization.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

MetaboCoreUtils defines metabolomics-related core functionality provided as low-level functions to allow a data structure-independent usage across various R packages. This includes functions to calculate between ion (adduct) and compound ma.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Implements a variety of methods for combining p-values in differential analyses of genome-scale datasets. Functions can combine p-values across different tests in the same analysis (e.g., genomic windows in ChIP-seq, exons in RNA-seq) or fo.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Identify significant miRNA-mRNA correlations across three or more time points using fold change data and background distribution comparisons.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progre.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Tools for LiP peptide and protein significance analysis. Provides functions for summarization, estimation of LiP peptide abundance, and detection of changes across conditions. Utilizes functionality across the MSstats family of packages.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

NanoTube includes functions for the processing, quality control, analysis, and visualization of NanoString nCounter data. Analysis functions include differential analysis and gene set analysis methods, as well as postprocessing steps to help understand the results. Additional functions are included to enable…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data. The method is based on nearest-neighbor Gaussian processes and uses the BRISC algorithm for model fitting and parameter estimation. Allows identification and ranking of SVGs with flexible length scales…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Skill "bioconductor-omicsviewer" from bioMate-AI/biomate-bioconductor-kb, covering omicsviewer, workflows, standard workflow, prepare the expressionset object and run correlation analysis and extend metadata.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

This packages provides C++ header files for developers wishing to create R packages that processes BAM files. ompBAM automates file access, memory management, and handling of multiple threads 'behind the scenes', so developers can focus on creating domain-specific functionality. The included vignette contains detailed…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

The ORFhunteR package is a R and C++ library for an automatic determination and annotation of open reading frames (ORF) in a large set of RNA molecules. It efficiently implements the machine learning model based on vectorization of nucleotide sequences and the random forest classification algorithm. The ORFhunteR…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Pathview is a stand-alone software package for pathway based data integration and visualization.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (variant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript sequences. The flexible workflow can be adopted to suit a myriad of research and…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

This package performs differential pattern analysis for Ribo-seq data. It identifies genes with significantly different patterns in the ribosome footprint between two conditions. RiboDiPA contains five major components including bam file processing, P-site mapping, data binning, differential pattern analysis and…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

A set of tools for working with miRNA affinity models (KdModels), efficiently scanning for miRNA binding sites, and predicting target repression. It supports scanning using miRNA seeds, full miRNA sequences (enabling 3' alignment) and KdModels, and includes the prediction of slicing and TDMD sites. Finally, it…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

The package comprises a set of pretrained machine learning models to predict basic immune cell types. This enables all users to quickly get a first annotation of the cell types present in their dataset without requiring prior knowledge. scAnnotatR also allows users to train their own models to predict new cell types…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Provides large-scale single-cell omics data manipulation using Genomic Data Structure (GDS) files. It combines dense and sparse matrices stored in GDS files and the Bioconductor infrastructure framework (SingleCellExperiment and DelayedArray) to provide out-of-memory data storage and large-scale manipulation using the…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control and visualization.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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…