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 RAE230B.

PhIPData defines an S4 class for phage-immunoprecipitation sequencing (PhIP-seq) experiments. Buliding upon the RangedSummarizedExperiment class, PhIPData enables users to coordinate metadata with experimental data in analyses. Additionally, PhIPData provides specialized methods to subset and identify beads-only samples, subset objects using virus aliases, and use existing peptide libraries to populate object parameters.

Platform Design Info for The Manufacturer's Name Bovine.

Base annotation databases for pig, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.

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.

Pirat enables the imputation of missing values (either MNARs or MCARs) in bottom-up LC-MS/MS proteomics data using a penalized maximum likelihood strategy. It does not require any parameter tuning, it models the instrument censorship from the data available. It accounts for sibling peptides correlations and it can leverage complementary transcriptomics measurements.

Platform Design Info for The Manufacturer's Name HG-U133B.

Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.

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

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

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

Platform Design Info for The Manufacturer's Name NuGO_Mm1a520177.

This package contains all the datasets used in the PepsNMR package.

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

Determining the sample size for adequate power to detect statistical significance is a crucial step at the design stage for high-throughput experiments. Even though a number of methods and tools are available for sample size calculation for microarray and RNA-seq in the context of differential expression (DE), this topic in the field of single-cell RNA sequencing is understudied. Moreover, the unique data characteristics present in scRNA-seq such as sparsity and heterogeneity increase the challenge. We propose POWSC, a simulation-based method, to provide power evaluation and sample size recommendation for single-cell RNA sequencing DE analysis. POWSC consists of a data simulator that creates realistic expression data, and a power assessor that provides a comprehensive evaluation and visualization of the power and sample size relationship.

Platform Design Info for Affymetrix Clariom_S_Human_HT.

Platform Design Info for The Manufacturer's Name HG_U95C.

Platform Design Info for The Manufacturer's Name E_coli_2.

Statistical analysis of peptide microarrays.

This package provides a Bioconductor data package for the Varambally dataset.

Platform Design Info for The Manufacturer's Name MG_U74Bv2.

Platform Design Info for The Manufacturer's Name Rice.

Platform Design Info for Affymetrix miRNA-3_0.