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@proteomicsyates

Yates lab

Yates lab - Proteomics Laboratory

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  1. PINT PINT Public

    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…

    Java 4 1

  2. ProteinClusterQuant ProteinClusterQuant Public

    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 visual…

    Python 6 3

  3. proteoform_dbIndex proteoform_dbIndex Public

    extension of dbIndex module to index proteoforms

    Java 1

  4. GlycoMSQuant GlycoMSQuant Public

    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 f…

    Java 3 1

  5. pctsea-parent pctsea-parent Public

    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 expre…

    Java 1

  6. utilities utilities Public

    General Java util classes used across different projects

    Java 1

Repositories

Showing 10 of 27 repositories
  • IP2_File_Transfer Public

    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/IP2_File_Transfer's past year of commit activity
    Java 0 Apache-2.0 0 0 1 Updated Apr 14, 2026
  • RawConverter Public Forked from YatesLab-Software-Repo/RawConverter

    RawConverter on proteomicsyates by the lab of John R. Yates III

    proteomicsyates/RawConverter's past year of commit activity
    C# 1 Apache-2.0 1 0 0 Updated Jan 12, 2025
  • PINT Public

    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 annotation…

    proteomicsyates/PINT's past year of commit activity
    Java 4 Apache-2.0 1 1 6 Updated Aug 6, 2024
  • utilities Public

    General Java util classes used across different projects

    proteomicsyates/utilities's past year of commit activity
    Java 0 Apache-2.0 1 0 4 Updated Aug 23, 2023
  • ProteinClusterQuant Public

    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/ProteinClusterQuant's past year of commit activity
    Python 6 3 0 0 Updated Aug 23, 2023
  • proteoform_dbIndex Public

    extension of dbIndex module to index proteoforms

    proteomicsyates/proteoform_dbIndex's past year of commit activity
    Java 0 Apache-2.0 1 0 0 Updated Aug 23, 2023
  • QuantParser Public

    Parser for quantitative data from files created by Census software.

    proteomicsyates/QuantParser's past year of commit activity
    Java 0 Apache-2.0 0 0 0 Updated Jun 16, 2023
  • dbIndex Public

    Indexing of FASTA files for searching peptide masses and sequences

    proteomicsyates/dbIndex's past year of commit activity
    Java 0 Apache-2.0 0 0 1 Updated May 23, 2023
  • ProteinAccessibilityCalculator Public

    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/ProteinAccessibilityCalculator's past year of commit activity
    Java 0 Apache-2.0 0 0 1 Updated Apr 17, 2023
  • mokapot Public Forked from wfondrie/mokapot

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

    proteomicsyates/mokapot's past year of commit activity
    Python 0 Apache-2.0 22 0 0 Updated Feb 10, 2023
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