Platform Design Info for The Manufacturer's Name HG_U95D.

Two experimental datasets to illustrate running and analysing phylogenetic profiles with PhyloProfile package.

Platform Design Info for Affymetrix MoGene-2_1-st.

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

The package is an R wrapper for Progenetix REST API built upon the Beacon v2 protocol. Its purpose is to provide a seamless way for retrieving genomic data from Progenetix database—an open resource dedicated to curated oncogenomic profiles. Empowered by this package, users can effortlessly access and visualize data from Progenetix.

Platform Design Info for The Manufacturer's Name MG_U74Av2.

This package provides methods and tools for (pre-)processing of metabolomics datasets (i.e. peak matrices), including filtering, normalisation, missing value imputation, scaling, and signal drift and batch effect correction methods. Filtering methods are based on: the fraction of missing values (across samples or features); Relative Standard Deviation (RSD) calculated from the Quality Control (QC) samples; the blank samples. Normalisation methods include Probabilistic Quotient Normalisation (PQN) and normalisation to total signal intensity. A unified user interface for several commonly used missing value imputation algorithms is also provided. Supported methods are: k-nearest neighbours (knn), random forests (rf), Bayesian PCA missing value estimator (bpca), mean or median value of the given feature and a constant small value. The generalised logarithm (glog) transformation algorithm is available to stabilise the variance across low and high intensity mass spectral features. Finally, this package provides an implementation of the Quality Control-Robust Spline Correction (QCRSC) algorithm for signal drift and batch effect correction of mass spectrometry-based datasets.

Platform Design Info for Affymetrix HuGene-2_0-st.

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

This package provides a package containing an environment representing the PrimeView.cdf file.

Platform Design Info for The Manufacturer's Name Zebrafish.

The package provides `rlang` data masks for the SummarizedExperiment class. The enables the evaluation of unquoted expression in different contexts of the SummarizedExperiment object with optional access to other contexts. The goal for `plyxp` is for evaluation to feel like a data.frame object without ever needing to unwind to a rectangular data.frame.

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

Platform Design Info for Affymetrix Clariom_D_Human.

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

Platform Design Info for The Manufacturer's Name RN_U34.

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

Platform Design Info for The Manufacturer's Name HG_U95A.

This package contains the function to assess the batch sourcs by fitting all "sources" as random effects including two-way interaction terms in the Mixed Model(depends on lme4 package) to selected principal components, which were obtained from the original data correlation matrix. This package accompanies the book "Batch Effects and Noise in Microarray Experiements, chapter 12.

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

Platform Design Info for The Manufacturer's Name HG_U95C.

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

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 Affymetrix miRNA-3_0.