Offers access to over 180 tools for the analysis of gene expression (RNA-seq and microarray), sequence variation and copy number, proteomic, flow cytometry, and network analysis. GenePattern is a genomic analysis platform that provides tools in the form of modules. Users can submit their data and choose suitable settings for performing complex analyses without detailed knowledge of the underlying programming language, algorithms and settings.
Aims to proteomics data analyses. Perseus extracts biologically meaningful information from processed raw files. It uses bioinformatic analyses from MaxQuant output and completes the proteomics analysis pipeline. It contains various statistical methods or illustrations (data transformation, normalization, imputation, and more). This tool gets five main interfaces: (1) data upload, (2) export, (3) processing, (4) analysis and (5) multimatrix handling.
Allows detection of differentially expressed features in molecular profiling experiments. RankProd is a non-parametric method that provides a robust and reliable implementation of the Rank Product (RP) methods. The software computes a user-defined number of random paired datasets and evaluates the RP or Rank Statistic (RS) per each of them. The method has also been integrated in the mzMatch pipeline.
A comprehensive suite to validate and quantify proteins by combining results from popular mass spectrometry platforms and database search engines. With dynamic extracted ion chromatogram plots, the ability to view every MS spectra at any time point and the ability to manually select a peak area, ProteoIQ® provides the ultimate level of control. ProteoIQ® provides a completely customizable interface to support any form of biological annotation. You can easily compare protein quantitative results in relation to biological pathways, protein localization, protein function, or even compare to transcript abundance. Every protein identification in ProteoIQ® can be linked to any external or internal knowledge database. Custom links are provided to GenBank, UniProt, IPI, and SwissProt databases or even an in-house LIMS.
Reads standard output from protein assemblies created by IDPicker, an HTML-based user interface to query shotgun proteomic data sets. QuasiTel allows users to automatically load the corresponding IDPicker summary file containing the number of confident identifications for each group used. Moreover, each user can select sets of mass spectrometry (MS) analyses to be compared and a minimum number of total spectral counts required across all groups for each protein.
A statistical framework with computational software tool for comparative quantitative proteomics analysis. QPROT features various extensions of QSPEC method originally built for spectral count data analysis, including probabilistic treatment of missing values in protein intensity data. With the increasing popularity of label-free quantitative proteomics data, the proposed method and accompanying software suite will be immediately useful for many proteomics laboratories.
Allows detailed, peptide-centric analysis of protein samples. Byologic enables researchers to characterize their product down to trace components. With this tool, flexible summary tables can generate reports for non-mass spec stakeholders for internal review, or for application filings. Moreover, it can compute extracted ion chromatograms (XICs) and relative abundances, and offers possibility to view and quantify peptides by XIC, TIC, and UV trace.