proteomicsyates/proteoform_dbIndex

extension of dbIndex module to index proteoforms

Language: Java - Size: 37.9 MB - Last synced: 2 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 1

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

Language: Java - Size: 327 KB - Last synced: 2 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

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).

Language: Python - Size: 319 MB - Last synced: 2 months ago - Pushed: 9 months ago - Stars: 5 - Forks: 3

proteomicsyates/mokapot Fork of wfondrie/mokapot

Fast and flexible semi-supervised learning for peptide detection in Python

Language: Python - Size: 58.6 MB - Last synced: 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

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.

Language: Java - Size: 1.72 MB - Last synced: 2 months ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

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).

Language: Java - Size: 23 MB - Last synced: 2 months ago - Pushed: over 1 year ago - Stars: 3 - Forks: 0

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).

Language: Java - Size: 18.5 MB - Last synced: 2 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

proteomicsyates/utilities

General Java util classes used across different projects

Language: Java - Size: 6.74 MB - Last synced: 2 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 1

proteomicsyates/QuantParser

Parser for quantitative data from files created by Census software.

Language: Java - Size: 796 KB - Last synced: 2 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 0

proteomicsyates/DTASelectParser

Java parser for DTASelect output files

Language: Java - Size: 97.7 KB - Last synced: 2 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

proteomicsyates/CensusTMT2MSstatsTMT

Converter from Census TMT output file to the input of MSstatsTMT

Language: Java - Size: 247 KB - Last synced: 2 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 1

proteomicsyates/ViSEAGO_Shiny

Language: R - Size: 57.6 KB - Last synced: 2 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

proteomicsyates/pcomplex

Language: Java - Size: 3.02 MB - Last synced: 2 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

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

Language: Java - Size: 69.3 KB - Last synced: 2 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

proteomicsyates/luciphor_dtaselect_integrator

Program that integrates results from Luciphor (PTM localization scoring algorithm) into DTASelect output files.

Language: Java - Size: 87.9 KB - Last synced: 2 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

proteomicsyates/dbIndex

Indexing of FASTA files for searching peptide masses and sequences

Language: Java - Size: 191 KB - Last synced: 2 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

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

Language: Java - Size: 133 KB - Last synced: 2 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

proteomicsyates/rt2dtaselect

Adds retention time to dtaselect output files, by reading it from ms2 (either in the local system or in a remote server)

Language: Java - Size: 13.7 KB - Last synced: 2 months ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

proteomicsyates/Dilu

Language: C - Size: 82.3 MB - Last synced: 2 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

proteomicsyates/PCQ_GUI

Size: 4.88 KB - Last synced: 2 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

proteomicsyates/P3

The Protein-Protein Predictor (P3) is a software for the prediction of real protein-protein interactions in multiple-bait IP-MS experiments

Language: Java - Size: 169 KB - Last synced: 2 months ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

proteomicsyates/DTASelect2PepXML

Converter from DTASelect to pepXML formats

Language: Java - Size: 37.1 KB - Last synced: 2 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

proteomicsyates/MzIdentMLParser

parser of mzIdentML files to read the data using the proteomics model from utilities artifact

Language: Java - Size: 2.23 MB - Last synced: 2 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

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.

Language: Java - Size: 15.9 MB - Last synced: 2 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

proteomicsyates/RadialTopologyViewer

RadialTopologyViewer performs a graphical visualization of a bait protein interactome derived from a co-immunoprecipitation experiment.

Language: Java - Size: 264 KB - Last synced: 2 months ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

proteomicsyates/CoPIT

Co-Purifying Protein Identification Technology (CoPIT) is a tool for the prediction of true interactors in single bait IP-MS

Size: 4.88 KB - Last synced: 2 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0