Platform Design Info for The Manufacturer's Name Barley1.

This package provides tools for large-scale protein motif analysis and visualization in R. PMScanR facilitates the identification of motifs using external tools like PROSITE's ps_scan (handling necessary file downloads and execution) and enables downstream analysis of results. Key features include parsing scan outputs, converting formats (e.g., to GFF-like structures), generating motif occurrence matrices, and creating informative visualizations such as heatmaps, sequence logos (via seqLogo/ggseqlogo). The package also offers an optional Shiny-based graphical user interface for interactive analysis, aiming to streamline the process of exploring motif patterns across multiple protein sequences.

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

Platform Design Info for Affymetrix MTA-1_0.

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.

Platform Design Info for The Manufacturer's Name Chicken.

Platform Design Info for Affymetrix HuGene-2_1-st.

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

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

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

Runs PANDA, an algorithm for discovering novel network structure by combining information from multiple complementary data sources.

Platform Design Info for The Manufacturer's Name HG_U95Av2.

This package provides a Bioconductor data package for the Taylor et al (2010) dataset.

Platform Design Info for NimbleGen 2006-10-31_rn34_refseq_promoter.

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

Platform Design Info for The Manufacturer's Name Citrus.

Platform Design Info for The Manufacturer's Name Rice.

Platform Design Info for Affymetrix CHOGene-2_1-st.

Use multiple factor analysis to calculate individualized pathway-centric scores of deviation with respect to the sampled population based on multi-omic assays (e.g., RNA-seq, copy number alterations, methylation, etc). Graphical and numerical outputs are provided to identify highly aberrant individuals for a particular pathway of interest, as well as the gene and omics drivers of aberrant multi-omic profiles.

Algorithm and tools for in silico pack-TYPE transposon discovery. Filters a given genome for properties unique to DNA transposons and provides tools for the investigation of returned matches. Sequences are input in DNAString format, and ranges are returned as a dataframe (in the format returned by as.dataframe(GRanges)).

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.

Package to predict protein-protein interaction (PPI) networks in target organisms for which only a view information about PPIs is available. Path2PPI predicts PPI networks based on sets of proteins which can belong to a certain pathway from well-established model organisms. It helps to combine and transfer information of a certain pathway or biological process from several reference organisms to one target organism. Path2PPI only depends on the sequence similarity of the involved proteins.

Platform Design Info for The Manufacturer's Name MOE430B.

Platform Design Info for Affymetrix HuEx-1_0-st-v2.