bioMate AI

topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and

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seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).

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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

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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

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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 data. This is done by computing similarity networks of biclusters and filtering for overlaps using a custom error model. After that, the louvain modularity it used to extract biclus

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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

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

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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

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