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

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.

This is a package that includes pre-processing and quality control functions that can remove margin events, compensate and transform the data and that will use PeacoQCSignalStability for quality control. This last function will first detect peaks in each channel of the flowframe. It will remove anomalies based on the IsolationTree function and the MAD outlier detection method. This package can be used for both flow- and mass cytometry data.

Platform Design Info for The Manufacturer's Name HG_U95B.

Phantasus is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus – a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported.

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

Platform Design Info for Affymetrix MoGene-1_0-st-v1.

Platform Design Info for The Manufacturer's Name miRNA-1_0.

Platform Design Info for The Manufacturer's Name HT_MG-430A.

It uses the overlap between enriched and non-enriched datasets to compensate for the bias introduced in global phosphorylation after applying median normalization.

Platform Design Info for Affymetrix MTA-1_0.

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.

CNV detection tool for targeted NGS panel data. Extension of the cn.mops package.

Platform Design Info for The Manufacturer's Name HG_U95D.

Significance assessment for distance measures of time-course protein profiles.

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

PrInCE (Predicting Interactomes from Co-Elution) uses a naive Bayes classifier trained on dataset-derived features to recover protein-protein interactions from co-elution chromatogram profiles. This package contains the R implementation of PrInCE.

Platform Design Info for The Manufacturer's Name Plasmodium_Anopheles.

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 Affymetrix GenomeWideSNP_6.

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

Platform Design Info for NimbleGen 2006-07-18_hg18_refseq_promoter.

Platform Design Info for Affymetrix RaEx-1_0-st-v1.

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.