FHCRC Nelson Lab pedbarrayv9 Annotation Data (pedbarrayv9) assembled using data from public repositories.

Two experimental datasets to illustrate running and analysing phylogenetic profiles with PhyloProfile package.

This R package helps the user identify k-mers (e.g. di- or tri-nucleotides) present periodically in a set of genomic loci (typically regulatory elements). The functions of this package provide a straightforward approach to find periodic occurrences of k-mers in DNA sequences, such as regulatory elements. It is not aimed at identifying motifs separated by a conserved distance; for this type of analysis, please visit MEME website.

Platform Design Info for The Manufacturer's Name RN_U34.

Platform Design Info for The Manufacturer's Name RAE230A.

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 The Manufacturer's Name Rice.

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.

Mapping PSMs back to genome. The package builds SAM file from shotgun proteomics data The package also provides function to prepare annotation from GTF file.

This package provides sample files and data for the vignettes of pepStat and Pviz as well as peptide collections for HIV and SIV.

This package provides a Bioconductor data package for the Ross-Adams (2015) Prostate Cancer dataset.

Platform Design Info for Affymetrix RaGene-1_0-st-v1.

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

This package provides kallisto workflow and transcript expression of RNA-Seq data from Brooks et al.

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

Platform Design Info for The Manufacturer's Name Pae_G1a.

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

This package provides functions to Analyze Microarray (Gene Expression) Data.

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

This package provides S4 classes and methods for inferring functional gene networks with edges encoding posterior beliefs of gene association types and nodes encoding perturbation effects.

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

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

Platform Design Info for The Manufacturer's Name Bovine.

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.