proteomics-data-analysis

There are 102 repositories under proteomics-data-analysis topic.

  • Olink-Proteomics/OlinkRPackage

    Olink R package: A collection of functions to facilitate analysis of proteomic data from Olink. The goal of this package is to help users extract biological insights from proteomic data run on the Olink platform.

    Language:R116107529

  • fgcz/prolfqua

    Differential Expression Analysis tool box R lang package for omics data

    Language:R464669

  • SomaLogic/SomaDataIO

    The SomaDataIO package loads and exports 'SomaScan' data via the 'SomaLogic Operating Co., Inc.' proprietary data file, called an ADAT ('*.adat'). The package also exports auxiliary functions for manipulating, wrangling, and extracting relevant information from an ADAT object once in memory.

    Language:R2778118

  • tbaccata/amica

    amica: an interactive and user-friendly web-based platform for the analysis of proteomics data

    Language:R273348

  • SlavovLab/DO-MS

    An modular and extensible app for visualization of mass spectrometry data and optimization of data acquisition.

    Language:R2531110
  • VolcaNoseR

    JoachimGoedhart/VolcaNoseR

    Shiny app for making and annotating Volcano plots

    Language:R242177
  • HistoJS

    Mmasoud1/HistoJS

    HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇

    Language:JavaScript23100

  • bigbio/sdrf-pipelines

    `sdrf-pipelines` is the official SDRF file validator and converts SDRF to pipeline configuration files

    Language:Python2199026

  • nwamsley1/Pioneer.jl

    CLI toolkit for fast analysis of DIA proteomics experiments and in silico library prediction

    Language:Julia191134

  • SlavovLab/SCP_recommendations

    Initial recommendations for performing, benchmarking, and reporting single-cell proteomics experiments. The code is distributed under an MIT license.

    Language:R12264

  • SlavovLab/plexDIA

    Multiplexed data-independent acquisition (plexDIA) for increasing proteomics throughput. The code is distributed by an MIT license.

    Language:R11362
  • autoprot

    ag-warscheid/autoprot

    autoprot provides standardised, fast, and reliable proteomics data analysis while ensuring a high customisability needed to tailor the analysis pipeline to specific experimental strategies.

    Language:Python101422

  • hds-sandbox/proteomics-sandbox

    A resource for biomedical students and researchers. Includes proteomics software tools like FragPipe, MaxQuant, PDV, SearchGUI, ThermoRawFileParser, and PeptideShaker. Offers a user-friendly interface, automated identification and quantification, comprehensive data analysis, and lightweight clone feature for optimized storage.

    Language:Jupyter Notebook10402

  • buenoalvezm/Pan-cancer-profiling

    This repository contains the code to reproduce our exploratory analysis of a pan-cancer plasma proteomics dataset, including differential expression analysis and disease classification (https://doi.org/10.1038/s41467-023-39765-y). The data can be explored in the Human Protein Atlas: www.proteinatlas.org/humanproteome/disease.

    Language:R9113

  • cox-labs/CoxLab_Bug_Reporting

    MaxQuant and Perseus Bug Reporting

    961521

  • breimanntools/xomics

    Python framework for explainable omics analysis

    Language:Jupyter Notebook7100

  • wulongict/SpectralArchive

    Visualization of spectral archive

    Language:C++7201

  • moritzmadern/Cassiopeia_LFQ

    R script to perform standard analysis steps for label-free proteomics data

    5102

  • SlavovLab/QuantQC

    QuantQC is a package for quality control (QC) of single-cell proteomics data. It is optimized to work with nPOP, a method for massively parallel sample preparation on glass slides.

    Language:HTML5122

  • SomaLogic/SomaScan.db

    An R package providing extended biological annotations for the SomaScan Assay, a proteomics platform developed by SomaLogic Operating Co., Inc.

    Language:R5382

  • czbiohub-sf/grassp

    GRaph-based Analysis of Subcellular/Spatial Proteomics

    Language:Python4

  • dev-ev/isobaric-inspection-jupyter

    Inspecting the quality of isobaric labeling proteomic data in a Jupyter notebook. Data output from Proteome Discoverer.

    Language:Jupyter Notebook3201

  • MateuszFido/LCMSpector

    📊 User-friendly mass spectrometry and chromatography data analysis app with native UI, graphing, quantification, MS/MS and data export capabilities

    Language:Python3

  • MiguelCos/Fragterminomics

    Annotation and processing of peptides from FragPipe search results

    Language:R31141
  • ProteinCleaverStreamlitApp

    pgarrett-scripps/ProteinCleaverStreamlitApp

    Protein Cleaver is a versatile tool for protein analysis and digestion.

    Language:Python3101

  • russelllab/wesa

    WeSA (Weighted SocioAffinity): a tool for improving affinity proteomics data.

    Language:HTML3200

  • SomaLogic/SomaPlotr

    A highly specialized suite of standardized plotting routines based on the "Grammar of Graphics" framework of mapping variables to aesthetics used in 'ggplot2'. Graphics types are biased towards visualizing SomaScan (proteomic) data.

    Language:R35224

  • symbioticMe/batch_effects_workflow_code

    Code accompanying batch effects processing workflow for "omic" data, mainly targeted for proteomics

    Language:R3202

  • bibs-lab/SpecGlobX

    SpecGlobX: java program that can be used when interpreting mass spectra in proteomics.

    Language:Java2320

  • daisybio/PRONE.Shiny

    Code of the R Shiny App of the PRONE R Package.

    Language:R214

  • lmboat/protein_structure_annotations

    Map residue numbers from experimental protein structures to primary protein sequences and calculate the relative solvent accessibility of each residue

    Language:Python2100

  • lmboat/residue_function_annotations

    Identify small-molecule sites of labeling that are annotated as active sites, binding sites, disulfide bonds and redox active sites

    Language:Jupyter Notebook2100

  • SamueldelaCamaraFuentes/TraianProt

    Pipeline and Shiny app for the dowstream analysis of quantitative proteomic data

    Language:R2100

  • seerbio/seer-pas-sdk

    Python SDK for Seer PAS

    Language:Python2000

  • SlavovLab/CellPermeability

    Cell Permeability analysis

    Language:R210

  • vaishnavpvarma/vaxijen-antigenicity-parser

    Automated parser for VaxiJen output 🚀 A lightweight Perl tool to extract and tabulate antigenicity predictions from VaxiJen . Designed for bioinformatics, immunoinformatics, and reverse vaccinology workflows, this script helps researchers process large datasets into clean, ready-to-analyze tables.

    Language:Perl2