Pinned Repositories
CensusTMT2MSstatsTMT
Converter from Census TMT output file to the input of MSstatsTMT
DTASelect2PepXML
Converter from DTASelect to pepXML formats
GlycoMSQuant
This is a Java stand-alone tool for the quantitation of glyco sites. It calculates the proportion of different glyco-PTMs in a protein of interest. It supports data from IP2 (quant compare output files) and MaxQuant.
luciphor_dtaselect_integrator
Program that integrates results from Luciphor (PTM localization scoring algorithm) into DTASelect output files.
pctsea-parent
PCTSEA (Proteomics Cell Type Enrichment Analysis) is a tool designed to statistically determine which cell types are significatively enriched in an input set of proteins with certain relative expression values. This process is done by using a database of datasets of RNASeq expression values from single cells from which the cell type is known (or predicted).
PINT
PINT is a new comprehensive web-based system to store, visualize, and query experimental proteomics data obtained under different experimental conditions and projects. PINT provides a very powerful query system through the use of different proteomics-specific data query commands running over both the experimental features and external annotations of the detected protein lists (such as UniprotKB).
ProteinClusterQuant
Protein Cluster Quant is a Java software for the analysis of complex proteomics samples (quantitative or not). It helps to reduce the redundancy of the peptide-to-protein relationship and to visualize the results in a bipartite network (Cytoscape).
proteoform_dbIndex
extension of dbIndex module to index proteoforms
utilities
General Java util classes used across different projects
ViSEAGO_Shiny
Yates lab's Repositories
proteomicsyates/ProteinClusterQuant
Protein Cluster Quant is a Java software for the analysis of complex proteomics samples (quantitative or not). It helps to reduce the redundancy of the peptide-to-protein relationship and to visualize the results in a bipartite network (Cytoscape).
proteomicsyates/PINT
PINT is a new comprehensive web-based system to store, visualize, and query experimental proteomics data obtained under different experimental conditions and projects. PINT provides a very powerful query system through the use of different proteomics-specific data query commands running over both the experimental features and external annotations of the detected protein lists (such as UniprotKB).
proteomicsyates/GlycoMSQuant
This is a Java stand-alone tool for the quantitation of glyco sites. It calculates the proportion of different glyco-PTMs in a protein of interest. It supports data from IP2 (quant compare output files) and MaxQuant.
proteomicsyates/CensusTMT2MSstatsTMT
Converter from Census TMT output file to the input of MSstatsTMT
proteomicsyates/DTASelect2PepXML
Converter from DTASelect to pepXML formats
proteomicsyates/IP2_File_Transfer
Giving some SSH credentials to a file server with the files of IP2, it will explore a given list of IP2 projects to get all RAW files and DTASelect files and transfer them to an external FTP site, such as MassIVE
proteomicsyates/luciphor_dtaselect_integrator
Program that integrates results from Luciphor (PTM localization scoring algorithm) into DTASelect output files.
proteomicsyates/pctsea-parent
PCTSEA (Proteomics Cell Type Enrichment Analysis) is a tool designed to statistically determine which cell types are significatively enriched in an input set of proteins with certain relative expression values. This process is done by using a database of datasets of RNASeq expression values from single cells from which the cell type is known (or predicted).
proteomicsyates/proteoform_dbIndex
extension of dbIndex module to index proteoforms
proteomicsyates/QuantParser
Parser for quantitative data from files created by Census software.
proteomicsyates/utilities
General Java util classes used across different projects
proteomicsyates/ViSEAGO_Shiny
proteomicsyates/CoPIT
Co-Purifying Protein Identification Technology (CoPIT) is a tool for the prediction of true interactors in single bait IP-MS
proteomicsyates/dbIndex
Indexing of FASTA files for searching peptide masses and sequences
proteomicsyates/Dilu
proteomicsyates/DTASelect2MzId
Data file format converter, from DTASelect-filter.txt files (output from DTASelect software) to mzIdentML version 1.1.0 and 1.2.0
proteomicsyates/DTASelectParser
Java parser for DTASelect output files
proteomicsyates/mokapot
Fast and flexible semi-supervised learning for peptide detection in Python
proteomicsyates/MzIdentMLParser
parser of mzIdentML files to read the data using the proteomics model from utilities artifact
proteomicsyates/P3
The Protein-Protein Predictor (P3) is a software for the prediction of real protein-protein interactions in multiple-bait IP-MS experiments
proteomicsyates/pcomplex
proteomicsyates/PCQ_GUI
proteomicsyates/ProteinAccessibilityCalculator
Based on Jmol, it calculates the surface accessibility of specific sites in a given protein. Optionally it measures the distances between specific atoms of specific sites in the structure of the protein
proteomicsyates/RadialTopologyViewer
RadialTopologyViewer performs a graphical visualization of a bait protein interactome derived from a co-immunoprecipitation experiment.
proteomicsyates/rt2dtaselect
Adds retention time to dtaselect output files, by reading it from ms2 (either in the local system or in a remote server)
proteomicsyates/TargetSeeker-MS
TargetSeeker-MS is a Bayesian Inference approach for drug target discovery, using protein fractionation coupled to mass spectrometry. It identifies proteins that are statistically significantly enriched via generating a noise-model using Bayesian Inference, which are measured with high reproducibility across a set of replicates.