Search Results for "trans-proteomic pipeline"

The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.

... in larger quantitation coverage, and the filter removes PSMs of larger quantitation error, retaining those of higher quantitation accuracy. The proposed pipeline is fully compatible with the Trans-Proteomic Pipeline and can be executed on Windows, Linux, and MacOS platforms.

CPFP provides a pipeline for the analysis of MS/MS proteomic data, targeted at the needs of central proteomics facilities. == Project Status - Updated January 3rd 2019 == CPFP has not been actively developed since 2014, when I left the proteomics group at UTSW. To access up-to-date algorithms for the analysis of proteomics data, other tools would now be preferred. However: * Limited fixes have been made on the main master branch by Phil Charles at the University of Oxford...

... hand, the biological information encoded in human genome, such as regulatory features from the Ensembl regulatory database, will be conductive in pinpointing functional causal variant(s) for the disease association. Thus, we generated a pipeline, PExFInS to integrate our LCL cis-eQTL data, along with publicly available cis-eQTL datasets derived from lung tissues, human monocytes, dendritic cells, blood, and LCLs.

A tool for extracting and preprocessing spectral count data for label-free quantitative proteomic analysis. This program is designed to be used with the Trans-Proteomic Pipeline (TPP).

APP automates and allows distributed computing of common proteomics tasks using a java-front end to provide both GUI and server parts. It is highly recommended for use with the Trans Proteomic Pipeline but this is not a requirement.

... pipeline started to appear: assemble reads with MIRA or SOAPdenovo-Trans, look for a scaffold/contig that matches a closely-related species, check it to see if all expected genomic features are present (since mitochondria is well conserved), check to see if the assembly might have circularized (since it's a circular DNA). If a feature was missing, or it hasn't circularized, try and assemble again with different assembler parameters (mainly k-mer). Rinse and repeat until the best build is found.

Luciphor is a program that performs phospho-site localization on MS/MS data processed by the Trans-Proteomic Pipeline (TPP). It is the first phospho-site prediction program to provide estimates for the false localization rate (FLR). The program is multithreaded and written in C++ for linux.