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

This package provides a toolkit of high-level functions for DNA motif scanning and enrichment analysis built upon Biostrings. The main functionality is PWM enrichment analysis of already known PWMs (e.g. from databases such as MotifDb), but the package also implements high-level functions for PWM scanning and visualisation. The package does not perform "de novo" motif discovery, but is instead focused on using motifs that are either experimentally derived or computationally constructed by other tools.

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

Platform Design Info for The Manufacturer's Name miRNA-1_0.

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.

Platform Design Info for Affymetrix RTA-1_0.

Platform Design Info for The Manufacturer's Name Vitis_Vinifera.

PAST takes GWAS output and assigns SNPs to genes, uses those genes to find pathways associated with the genes, and plots pathways based on significance. Implements methods for reading GWAS input data, finding genes associated with SNPs, calculating enrichment score and significance of pathways, and plotting pathways.

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 Poplar\_probe\_tab.

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.

This package is a gene/phenotype prioritization tool that utilizes multiplex heterogeneous gene phenotype network. PhenoGeneRanker allows multi-layer gene and phenotype networks. It also calculates empirical p-values of gene/phenotype ranking using random stratified sampling of genes/phenotypes based on their connectivity degree in the network. https://dl.acm.org/doi/10.1145/3307339.3342155.

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

Platform Design Info for The Manufacturer's Name HT_HG-U133_Plus_PM.

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

Platform Design Info for The Manufacturer's Name MG_U74A.

Platform Design Info for The Manufacturer's Name Zebrafish.

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

Platform Design Info for The Manufacturer's Name X_laevis_2.

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

The PIUMA package offers a tidy pipeline of Topological Data Analysis frameworks to identify and characterize communities in high and heterogeneous dimensional data.

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

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

The package allows for predicting whether a coiled coil sequence (amino acid sequence plus heptad register) is more likely to form a dimer or more likely to form a trimer. Additionally to the prediction itself, a prediction profile is computed which allows for determining the strengths to which the individual residues are indicative for either class. Prediction profiles can also be visualized as curves or heatmaps.

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