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.

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

This package provides a Bayesian method for quantifying the liklihood that a given plasma mutation arises from clonal hematopoesis or the underlying tumor. It requires sequencing data of the mutation in plasma and white blood cells with the number of distinct and mutant reads in both tissues. We implement a Monte Carlo importance sampling method to assess the likelihood that a mutation arises from the tumor relative to non-tumor origin.

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

The Parallel Mixed Model (PMM) approach is suitable for hit selection and cross-comparison of RNAi screens generated in experiments that are performed in parallel under several conditions. For example, we could think of the measurements or readouts from cells under RNAi knock-down, which are infected with several pathogens or which are grown from different cell lines.

Runs PANDA, an algorithm for discovering novel network structure by combining information from multiple complementary data sources.

This package provides tools to test correlation between gene expression and phenotype in a way that is efficient, structured, fast and scalable. GSEA is also provided.

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

This package provides support for parallelized estimation of GLMs/GEEs, catering for dispersed data.

Platform Design Info for The Manufacturer's Name S_aureus.

Platform Design Info for Affymetrix miRNA-3_1.

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.

This package provides a general tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables as described in Pounds et. al. (2009) Bioinformatics 25: 2013-2019.

Interactions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated with other proteins and other biomolecules. This fact has motivated the development of a variety of experimental methods for the identification of protein interactions. This variety has in turn ushered in the development of numerous different computational approaches for modeling and predicting protein interactions. Sometimes an experiment is aimed at identifying proteins closely related to some interesting proteins. A network based statistical learning method is used to infer the putative functions of proteins from the known functions of its neighboring proteins on a PPI network. This package identifies such proteins often involved in the same or similar biological functions.

Platform Design Info for The Manufacturer's Name Yeast_2.

Platform Design Info for The Manufacturer's Name RAE230A.

The package contains the function for filtering genes by the proportion of variation accounted for by the first principal component (PVAC).

This is a supplemental data package for the plotgardener package. Includes example datasets used in plotgardener vignettes and example raw data files. For details on how to use these datasets, see the plotgardener package vignettes.

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

Platform Design Info for The Manufacturer's Name Canine_2.

This package provides a Bioconductor data package for the Grasso (2012) Prostate Cancer dataset.

Platform Design Info for Affymetrix Mapping250K_Nsp.

Platform Design Info for The Manufacturer's Name ATH1-121501.

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.