bioMate-AI/biomate-bioconductor-kb

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Client for the gypsum REST API (https://gypsum.artifactdb.com), a cloud-based file store in the ArtifactDB ecosystem. This package provides functions for uploads, downloads, and various adminstrative and management tasks. Check out the docu.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

MHC (major histocompatibility complex) molecules are cell surface complexes that present antigens to T cells. The repertoire of antigens presented in a given genetic background largely depends on the sequence of the encoded MHC molecules, and thus, in humans, on the highly variable HLA (human leukocyte antigen) genes…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

This package is a implementation of biclustering ensemble method MoSBi (Molecular signature Identification from Biclustering). MoSBi provides standardized interfaces for biclustering results and can combine their results with a multi-algorithm ensemble approach to compute robust ensemble biclusters on molecular omics…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Harmonize data management of multiple experimental assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from SummarizedExperiment, supporting an open-ended mix of st.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA o.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Provides delayed computation of a matrix of residuals after fitting a linear model to each column of an input matrix. Also supports partial computation of residuals where selected factors are to be preserved in the output matrix. Implements.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

This skill is the knowledge layer — when, why, and how to use seqlogo. To run this analysis on your own data with managed compute, automated QC, and reproducible outputs, use BioMate — free to start.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

This skill is the knowledge layer — when, why, and how to use topgo. To run this analysis on your own data with managed compute, automated QC, and reproducible outputs, use BioMate — free to start.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

This tool uses the label-tree function from HyPhy to annotate a phylogenetic tree. It allows users to select a subset of leaves using either a regular expression or a list of sequence names, and then apply a specified label to these selecte.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

BEER implements a Bayesian model for analyzing phage-immunoprecipitation sequencing (PhIP-seq) data. Given a PhIPData object, BEER returns posterior probabilities of enriched antibody responses, point estimates for the relative fold-change in comparison to negative control samples, and more. Additionally, BEER…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Infrastructure to support 'views' used to classify Bioconductor packages. 'biocViews' are directed acyclic graphs of terms from a controlled vocabulary. There are three major classifications, corresponding to 'software', 'annotation', and '.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Infrastructure shared by all the Biostrings-based genome data packages.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

This package supports functional characteristics of both coding and non-coding genomics data for thousands of species with up-to-date gene annotation. It provides a univeral interface for gene functional annotation from a variety of sources.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Assess genome assembly and annotation quality by comparing custom statistics against NCBI genomes and evaluating gene space completeness with BUSCO.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

This skill is the knowledge layer — when, why, and how to use consensusclusterplus. To run this analysis on your own data with managed compute, automated QC, and reproducible outputs, use BioMate — free to start.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

A toolset for deciphering and managing biological sequences.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Skill "bioconductor-doubletrouble" from bioMate-AI/biomate-bioconductor-kb, covering doubletrouble, workflows, standard workflow, load example data and prepare input data.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working wit.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a.