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This package provides S4 classes and methods for inferring functional gene networks with edges encoding posterior beliefs of gene association types and nodes encoding perturbation effects.
Platform Design Info for The Manufacturer's Name Vitis_Vinifera.
Platform Design Info for The Manufacturer's Name HG_U95Av2.
This package provides support for parallelized estimation of GLMs/GEEs, catering for dispersed data.
Platform Design Info for The Manufacturer's Name HG_U95B.
Pathifier is an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample.
PhILR is short for Phylogenetic Isometric Log-Ratio Transform. This package provides functions for the analysis of compositional data (e.g., data representing proportions of different variables/parts). Specifically this package allows analysis of compositional data where the parts can be related through a phylogenetic tree (as is common in microbiota survey data) and makes available the Isometric Log Ratio transform built from the phylogenetic tree and utilizing a weighted reference measure.
Sample data for PREDA package. (annotations objects synchronized with GeneAnnot custom CDFs version 2.2.0).
Platform Design Info for The Manufacturer's Name HG-U219.
Platform Design Info for Affymetrix GuiGene-1_0-st.
Platform Design Info for The Manufacturer's Name Barley1.
This R package helps the user identify k-mers (e.g. di- or tri-nucleotides) present periodically in a set of genomic loci (typically regulatory elements). The functions of this package provide a straightforward approach to find periodic occurrences of k-mers in DNA sequences, such as regulatory elements. It is not aimed at identifying motifs separated by a conserved distance; for this type of analysis, please visit MEME website.
This package provides a Bioconductor data package for the Taylor et al (2010) dataset.
Platform Design Info for The Manufacturer's Name HC_G110.
CNV detection tool for targeted NGS panel data. Extension of the cn.mops package.
This package is a gene/phenotype prioritization tool that utilizes multiplex heterogeneous gene phenotype network. PhenoGeneRanker allows multi-layer gene and phenotype networks. It also calculates empirical p-values of gene/phenotype ranking using random stratified sampling of genes/phenotypes based on their connectivity degree in the network. https://dl.acm.org/doi/10.1145/3307339.3342155.
Platform Design Info for The Manufacturer's Name HT_HG-U133A.
This package provides sample files and data for the vignettes of pepStat and Pviz as well as peptide collections for HIV and SIV.
Implemented temporal PageRank analysis as defined by Rozenshtein and Gionis. Implemented multiplex PageRank as defined by Halu et al. Applied temporal and multiplex PageRank in gene regulatory network analysis.
PWMEnrich pre-compiled background objects for Drosophila melanogaster and MotifDb D. melanogaster motifs.
Platform Design Info for The Manufacturer's Name Poplar.
Platform Design Info for Affymetrix CyRGene-1_0-st.
The POMA package offers a comprehensive toolkit designed for omics data analysis, streamlining the process from initial visualization to final statistical analysis. Its primary goal is to simplify and unify the various steps involved in omics data processing, making it more accessible and manageable within a single, intuitive R package. Emphasizing on reproducibility and user-friendliness, POMA leverages the standardized SummarizedExperiment class from Bioconductor, ensuring seamless integration and compatibility with a wide array of Bioconductor tools. This approach guarantees maximum flexibility and replicability, making POMA an essential asset for researchers handling omics datasets. See https://github.com/pcastellanoescuder/POMAShiny. Paper: Castellano-Escuder et al. (2021) <doi:10.1371/journal.pcbi.1009148> for more details.
Platform Design Info for The Manufacturer's Name Ecoli_ASv2.