PanomiR is a package to detect miRNAs that target groups of pathways from gene expression data. This package provides functionality for generating pathway activity profiles, determining differentially activated pathways between user-specified conditions, determining clusters of pathways via the PCxN package, and generating miRNAs targeting clusters of pathways. These function can be used separately or sequentially to analyze RNA-Seq data.

Platform Design Info for The Manufacturer's Name Vitis_Vinifera.

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

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

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.

PartheenMetaData http://swegene.onk.lu.se Annotation Data (PartheenMetaData) assembled using data from public repositories.

Store UCSC phastCons conservation scores for the human genome (hg38) calculated from multiple alignments with other 99 vertebrate species.

Platform Design Info for The Manufacturer's Name Yeast_2.

Platform Design Info for Affymetrix Cytogenetics_Array.

PhantasusLite – a lightweight package with helper functions of general interest extracted from phantasus package. In parituclar it simplifies working with public RNA-seq datasets from GEO by providing access to the remote HSDS repository with the precomputed gene counts from ARCHS4 and DEE2 projects.

Platform Design Info for NimbleGen 2006-07-18_mm8_refseq_promoter.

Pviz adapts the Gviz package for protein sequences and data.

Calculates Probe-level Expression Change Averages (PECA) to identify differential expression in Affymetrix gene expression microarray studies or in proteomic studies using peptide-level mesurements respectively.

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 MG_U74B.

Implemented temporal PageRank analysis as defined by Rozenshtein and Gionis. Implemented multiplex PageRank as defined by Halu et al. Applied temporal and multiplex PageRank in gene regulatory network analysis.

Platform Design Info for The Manufacturer's Name NuGO_Mm1a520177.

Platform Design Info for The Manufacturer's Name MG_U74Bv2.

The package ptairData contains two raw datasets from Proton-Transfer-Reaction Time-of-Flight mass spectrometer acquisitions (PTR-TOF-MS), in the HDF5 format. One from the exhaled air of two volunteer healthy individuals with three replicates, and one from the cell culture headspace from two mycobacteria species and one control (culture medium only) with two replicates. Those datasets are used in the examples and in the vignette of the ptairMS package (PTR-TOF-MS data pre-processing). There are also used to gererate the ptrSet in the ptairMS data : exhaledPtrset and mycobacteriaSet.

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.

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

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

This package provides a package for processing protein mass spectrometry data.

Platform Design Info for The Manufacturer's Name AG.