Search Results for "trans-proteomic pipeline"
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Showing 11 open source projects for "trans-proteomic pipeline"
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... 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.
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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.
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Central Proteomics Facilities Pipeline
A data analysis pipeline for shotgun mass-spectrometry proteomics.
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. * As of 2019... -
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PExFInS
Post-GWAS Explorer for Functional Indels and SNPs
... 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. -
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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).
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Automated Proteomics Pipeline
A front end for several popular open source proteomics tools
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. -
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mitoMaker
mitoMaker - a mitochondria pipeline wrapper script
Mitomaker is a pipeline wrapper, result analyzer and automated annotator, written in Python v2.7, that, with the help of other programs, builds, analyzes, looks for the best build and annotates target genomes (such as mitochondria and cloroplast). It could be used with other targets, such as specific genes, or transcriptomes, even though that is not it's primary goal, nor thoroughly tested. After various attempts to build different mitochondrial genomes in the lab I studied, a general pipeline... -
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luciphor
Calculates phospho-site localizations
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. -
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This program parses data out of the interact*.xml files generated by the Trans-Proteomic Pipeline (TPP). It reads in a folder of such files and either makes a tab-delimited file or loads the data into a MySQL database.
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Attn: the latest version of ProteinProphet must be obtained as part of the Trans-Proteomic Pipeline package at http://sourceforge.net/projects/sashimi/.
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Attn: the latest version of PeptideProphet must be obtained as part of the Trans-Proteomic Pipeline package at http://sourceforge.net/projects/sashimi/.
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