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BigBio Stack

Provide big data solutions Bioinformatics

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  1. py-pgatk py-pgatk Public

    Python tools for proteogenomics analysis toolkit

    Python 10 11

  2. proteomics-sample-metadata proteomics-sample-metadata Public

    The Proteomics Experimental Design file format: Standard for experimental design annotation

    Python 75 106

  3. pepgenome pepgenome Public

    Proteogenomics tool that enables to map peptides to genome coordinates

    Java 3

  4. quantms quantms Public

    Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.

    Nextflow 26 35

  5. sparkms sparkms Public

    Spark package to perform downstream analysis of big data proteomics

    Python 3 2

Repositories

Showing 10 of 43 repositories
  • quantms Public

    Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.

    bigbio/quantms’s past year of commit activity
    Nextflow 26 MIT 35 50 (3 issues need help) 1 Updated Aug 17, 2024
  • quantms-utils Public

    A python library with scripts and helpers classes for quantms workflow

    bigbio/quantms-utils’s past year of commit activity
    Python 2 MIT 1 0 0 Updated Aug 16, 2024
  • quantms.io Public

    The proteomics quantification format, extending mzTab for large scale datasets.

    bigbio/quantms.io’s past year of commit activity
    Python 5 3 16 (1 issue needs help) 0 Updated Aug 14, 2024
  • sdrf-pipelines Public

    A repository to convert SDRF proteomics files into pipelines config files

    bigbio/sdrf-pipelines’s past year of commit activity
    Python 16 Apache-2.0 21 22 (5 issues need help) 0 Updated Aug 5, 2024
  • pmultiqc Public

    A library for QC report based on MultiQC framework

    bigbio/pmultiqc’s past year of commit activity
    Python 13 GPL-3.0 8 7 (1 issue needs help) 0 Updated Aug 2, 2024
  • DLEAMSE Public

    A Deep LEArning-based Mass Spectra Embedder for spectral similarity scoring

    bigbio/DLEAMSE’s past year of commit activity
    Python 11 Apache-2.0 4 3 0 Updated Jul 28, 2024
  • sdrf-utils Public

    sdrf-cls

    bigbio/sdrf-utils’s past year of commit activity
    Python 0 Apache-2.0 1 0 0 Updated Jul 4, 2024
  • pyspectrafuse Public

    Python library with utility scripts for spectrafuse pipeline

    bigbio/pyspectrafuse’s past year of commit activity
    Python 0 Apache-2.0 1 0 0 Updated Jun 26, 2024
  • fsspark Public

    Spark library for feature selection in multiomics using

    bigbio/fsspark’s past year of commit activity
    Python 1 Apache-2.0 1 4 (1 issue needs help) 0 Updated Jun 26, 2024
  • ibaqpy Public

    Absolute quantification package based on quantms.io

    bigbio/ibaqpy’s past year of commit activity
    Python 8 GPL-3.0 7 8 (2 issues need help) 0 Updated Jun 15, 2024
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