Platform Design Info for The Manufacturer's Name MOE430A.

Provide simple utilities for querying bhklab PharmacoDB, modeling API outputs, and integrating to cell and compound ontologies.

Platform Design Info for The Manufacturer's Name NuGO_Hs1a520180.

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).

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.

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

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

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

Publicly available RNA-seq data is routinely used for retrospective analysis to elucidate new biology. Novel transcript discovery enabled by large collections of RNA-seq datasets has emerged as one of such analysis. To increase the power of transcript discovery from large collections of RNA-seq datasets, we developed a new R package named Pooling RNA-seq and Assembling Models (PRAM), which builds transcript models in intergenic regions from pooled RNA-seq datasets. This package includes functions for defining intergenic regions, extracting and pooling related RNA-seq alignments, predicting, selected, and evaluating transcript models.

Platform Design Info for The Manufacturer's Name HG-U133A.

Platform Design Info for The Manufacturer's Name Xenopus_laevis.

Parsing pepXML files based one XML package. The package tries to handle pepXML files generated from different softwares. The output will be a peptide-spectrum-matching tabular file. The package also provide function to filter the PSMs based on FDR.

ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (variant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript sequences. The flexible workflow can be adopted to suit a myriad of research and experimental settings.

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

Operate on `GInteractions` objects as tabular data using `dplyr`-like verbs. The functions and methods in `plyinteractions` provide a grammatical approach to manipulate `GInteractions`, to facilitate their integration in genomic analysis workflows.

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

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

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

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.

This package provides sample files and data for the vignettes of pepStat and Pviz as well as peptide collections for HIV and SIV.

Platform Design Info for The Manufacturer's Name HG_U95D.

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

Platform Design Info for The Manufacturer's Name Soybean.

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.