Platform Design Info for The Manufacturer's Name MG_U74Cv2.

peakCombiner, a fully R based, user-friendly, transparent, and customizable tool that allows even novice R users to create a high-quality consensus peak list. The modularity of its functions allows an easy way to optimize input and output data. A broad range of accepted input data formats can be used to create a consensus peak set that can be exported to a file or used as the starting point for most downstream peak analyses.

Platform Design Info for The Manufacturer's Name Maize.

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 HG-Focus.

Pigengene package provides an efficient way to infer biological signatures from gene expression profiles. The signatures are independent from the underlying platform, e.g., the input can be microarray or RNA Seq data. It can even infer the signatures using data from one platform, and evaluate them on the other. Pigengene identifies the modules (clusters) of highly coexpressed genes using coexpression network analysis, summarizes the biological information of each module in an eigengene, learns a Bayesian network that models the probabilistic dependencies between modules, and builds a decision tree based on the expression of eigengenes.

This package uses a statistical framework for rapid and accurate detection of aneuploid cells with local copy number deletion or amplification. Our method uses an EM algorithm with mixtures of Poisson distributions while incorporating cytogenetics information (e.g., regional deletion or amplification) to guide the classification (partCNV). When applicable, we further improve the accuracy by integrating a Hidden Markov Model for feature selection (partCNVH).

Platform Design Info for The Manufacturer's Name Tomato.

Platform Design Info for The Manufacturer's Name DrosGenome1.

Platform Design Info for Affymetrix SoyGene-1_0-st.

Platform Design Info for Affymetrix FelGene-1_0-st.

Interactive R package with an intuitive Shiny-based graphical interface for alternative splicing quantification and integrative analyses of alternative splicing and gene expression based on The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression project (GTEx), Sequence Read Archive (SRA) and user-provided data. The tool interactively performs survival, dimensionality reduction and median- and variance-based differential splicing and gene expression analyses that benefit from the incorporation of clinical and molecular sample-associated features (such as tumour stage or survival). Interactive visual access to genomic mapping and functional annotation of selected alternative splicing events is also included.

Platform Design Info for Affymetrix CyRGene-1_1-st.

Platform Design Info for Affymetrix Mapping250K_Nsp.

Platform Design Info for The Manufacturer's Name Mu11KsubB.

Platform Design Info for The Manufacturer's Name Sugar_Cane.

Peptide Set Test (PepSetTest) is a peptide-centric strategy to infer differentially expressed proteins in LC-MS/MS proteomics data. This test detects coordinated changes in the expression of peptides originating from the same protein and compares these changes against the rest of the peptidome. Compared to traditional aggregation-based approaches, the peptide set test demonstrates improved statistical power, yet controlling the Type I error rate correctly in most cases. This test can be valuable for discovering novel biomarkers and prioritizing drug targets, especially when the direct application of statistical analysis to protein data fails to provide substantial insights.

Base annotation databases for pig, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.

Platform Design Info for The Manufacturer's Name AG.

Platform Design Info for The Manufacturer's Name HG-U133A_2.

This package contains a set of functions to perform large-scale analysis of pharmaco-genomic data. These include the PharmacoSet object for storing the results of pharmacogenomic experiments, as well as a number of functions for computing common summaries of drug-dose response and correlating them with the molecular features in a cancer cell-line.

This package contains R functions to predict biological variables to from placnetal DNA methylation data generated from infinium arrays. This includes inferring ethnicity/ancestry, gestational age, and cell composition from placental DNA methylation array (450k/850k) data.

Platform Design Info for The Manufacturer's Name Medicago.

Pirat enables the imputation of missing values (either MNARs or MCARs) in bottom-up LC-MS/MS proteomics data using a penalized maximum likelihood strategy. It does not require any parameter tuning, it models the instrument censorship from the data available. It accounts for sibling peptides correlations and it can leverage complementary transcriptomics measurements.