PathMED is a collection of tools to facilitate precision medicine studies with omics data (e.g. transcriptomics). Among its funcionalities, genesets scores for individual samples may be calculated with several methods. These scores may be used to train machine learning models and to predict clinical features on new data. For this, several machine learning methods are evaluated in order to select the best method based on internal validation and to tune the hyperparameters. Performance metrics and a ready-to-use model to predict the outcomes for new patients are returned.

Platform Design Info for The Manufacturer's Name AG.

Polytect is an advanced computational tool designed for the analysis of multi-color digital PCR data. It provides automatic clustering and labeling of partitions into distinct groups based on clusters first identified by the flowPeaks algorithm. Polytect is particularly useful for researchers in molecular biology and bioinformatics, enabling them to gain deeper insights into their experimental results through precise partition classification and data visualization.

This package provides functions for the projection of data into the spaces defined by PCA, CoGAPS, NMF, correlation, and clustering.

PWMEnrich pre-compiled background objects for M.musculus (mouse) and MotifDb M. musculus motifs.

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

Affymetrix Affymetrix Porcine Array annotation data (chip porcine) assembled using data from public repositories.

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

This package provides a Bioconductor data package for the Ross-Adams (2015) Prostate Cancer dataset.

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

Store UCSC phastCons mm39 conservation scores AnnotationHub Resource Metadata. Provide provenance and citation information for UCSC phastCons mm39 conservation score AnnotationHub resources. Illustrate in a vignette how to access those resources.

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.

Platform Design Info for The Manufacturer's Name Canine_2.

Platform Design Info for Affymetrix MoGene-1_1-st-v1.

Combine generalised least squares methodology from the nlme package for dealing with autocorrelation with penalised least squares methods from the glmnet package to deal with high dimensionality. This pengls packages glues them together through an iterative loop. The resulting method is applicable to high dimensional datasets that exhibit autocorrelation, such as spatial or temporal data.

Platform Design Info for The Manufacturer's Name Sugar_Cane.

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

This package provides a fast, convenient tool to identify the TSSs of miRNAs by integrating the data of H3K4me3 and Pol II as well as combining the conservation level and sequence feature, provided within both command-line and graphical interfaces, which achieves a better performance than the previous non-cell-specific methods on miRNA TSSs.

Platform Design Info for Affymetrix HTA-2_0.

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.

Platform Design Info for The Manufacturer's Name HG-U133_Plus_2.

Reads files exported from QX Manager or QuantaSoft containing amplitude values from a run of ddPCR (96 well plate) and robustly sets thresholds to determine positive droplets for each channel of each individual well. Concentration and normalized concentration in addition to other metrics is then calculated for each well. Results are returned as a table, optionally written to file, as well as optional plots (scatterplot and histogram) for both channels per well written to file. The package includes a shiny application which provides an interactive and user-friendly interface to the full functionality of PoDCall.

Platform Design Info for The Manufacturer's Name Canine.

Platform Design Info for The Manufacturer's Name Xenopus_laevis.