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Platform Design Info for Affymetrix miRNA-2_0.
Platform Design Info for Affymetrix Clariom_S_Mouse_HT.
Platform Design Info for The Manufacturer's Name ATH1-121501.
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.
Parsing pepXML files based one XML package. The package tries to handle pepXML files generated from different softwares. The output will be a peptide-spectrum-matching tabular file. The package also provide function to filter the PSMs based on FDR.
Platform Design Info for The Manufacturer's Name Chicken.
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 MoGene-2_1-st.
Platform Design Info for The Manufacturer's Name HG_U95Av2.
Platform Design Info for Affymetrix ChiGene-1_0-st.
Platform Design Info for Affymetrix RJpGene-1_1-st.
Platform Design Info for NimbleGen hg18_60mer_expr.
Protein Group Code Algorithm (PGCA) is a computationally inexpensive algorithm to merge protein summaries from multiple experimental quantitative proteomics data. The algorithm connects two or more groups with overlapping accession numbers. In some cases, pairwise groups are mutually exclusive but they may still be connected by another group (or set of groups) with overlapping accession numbers. Thus, groups created by PGCA from multiple experimental runs (i.e., global groups) are called "connected" groups. These identified global protein groups enable the analysis of quantitative data available for protein groups instead of unique protein identifiers.
Platform Design Info for Affymetrix CynGene-1_1-st.
Platform Design Info for Affymetrix Clariom_S_Mouse.
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.
This package provides a Bioconductor data package for the Ross-Adams (2015) Prostate Cancer dataset.
Platform Design Info for NimbleGen 2006-07-18_hg18_refseq_promoter.
This package provides a data package of SELDI-TOF protein mass spectrometry data of 167 breast cancer and normal samples.
Platform Design Info for Affymetrix MarGene-1_0-st.
Platform Design Info for The Manufacturer's Name Poplar.
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 P\_aeg1a\_probe\_tab.
Platform Design Info for The Manufacturer's Name HG-U219.
Platform Design Info for The Manufacturer's Name Vitis_Vinifera.