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.

PWMEnrich pre-compiled background objects for Drosophila melanogaster and MotifDb D. melanogaster motifs.

Platform Design Info for The Manufacturer's Name MG_U74B.

Platform Design Info for Affymetrix miRNA-3_0.

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

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

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

The package pRolocGUI comprises functions to interactively visualise spatial proteomics data on the basis of pRoloc, pRolocdata and shiny.

Platform Design Info for The Manufacturer's Name Ecoli_ASv2.

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.

Platform Design Info for The Manufacturer's Name Canine_2.

Platform Design Info for The Manufacturer's Name Porcine.

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

This package provides a set of annotation maps describing the entire Gene Ontology assembled using data from PANTHER.

Most human genes have multiple promoters that control the expression of different isoforms. The use of these alternative promoters enables the regulation of isoform expression pre-transcriptionally. Alternative promoters have been found to be important in a wide number of cell types and diseases. proActiv is an R package that enables the analysis of promoters from RNA-seq data. proActiv uses aligned reads as input, and generates counts and normalized promoter activity estimates for each annotated promoter. In particular, proActiv accepts junction files from TopHat2 or STAR or BAM files as inputs. These estimates can then be used to identify which promoter is active, which promoter is inactive, and which promoters change their activity across conditions. proActiv also allows visualization of promoter activity across conditions.

Platform Design Info for Affymetrix Cytogenetics_Array.

The ProteinGymR package provides analysis-ready data resources from ProteinGym, generated by Notin et al., 2023, as well as built-in functionality to visualize the data. ProteinGym comprises a collection of benchmarks for evaluating the performance of models predicting the effect of point mutations. This package provides access to 1. deep mutational scanning (DMS) scores from 217 assays measuring the impact of all possible amino acid substitutions across 186 proteins, 2. model performance metrics and prediction scores from 79 variant prediction models in the zero-shot setting and 12 models in the semi-supervised setting.

Platform Design Info for The Manufacturer's Name HG-U133_Plus_2.

Platform Design Info for The Manufacturer's Name Tomato.

Platform Design Info for The Manufacturer's Name Poplar.

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

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

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Plasmodium\_Anopheles\_probe\_tab.

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