proteomics-data-analysis | Topic

Topic: "proteomics-data-analysis"

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: R - Size: 731 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 108 - Forks: 27

fgcz/prolfqua

Differential Expression Analysis tool box R lang package for omics data

Language: R - Size: 762 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 40 - Forks: 7

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: R - Size: 28.1 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 25 - Forks: 18

tbaccata/amica

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

Language: R - Size: 24.1 MB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 24 - Forks: 8

SlavovLab/DO-MS

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

Language: R - Size: 17.3 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 24 - Forks: 8

JoachimGoedhart/VolcaNoseR

Shiny app for making and annotating Volcano plots

Language: R - Size: 485 KB - Last synced at: 5 months ago - Pushed at: 8 months ago - Stars: 21 - Forks: 7

bigbio/sdrf-pipelines

A repository to convert SDRF proteomics files into pipelines config files

Language: Python - Size: 60.8 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 19 - Forks: 25

Mmasoud1/HistoJS

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

Language: JavaScript - Size: 290 MB - Last synced at: 3 days ago - Pushed at: about 1 year ago - Stars: 19 - Forks: 0

SlavovLab/plexDIA

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

Language: R - Size: 27.1 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 11 - Forks: 2

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 Notebook - Size: 11.7 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 10 - Forks: 2

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: Python - Size: 234 MB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 9 - Forks: 2

cox-labs/CoxLab_Bug_Reporting

MaxQuant and Perseus Bug Reporting

Size: 24.4 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 7 - Forks: 1

breimanntools/xomics

Python framework for explainable omics analysis

Language: Jupyter Notebook - Size: 16.2 MB - Last synced at: 19 days ago - Pushed at: 9 months ago - Stars: 7 - Forks: 0

wulongict/SpectralArchive

Visualization of spectral archive

Language: C++ - Size: 132 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 5 - Forks: 2

moritzmadern/Cassiopeia_LFQ

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

Size: 19.5 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 5 - Forks: 2

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: HTML - Size: 34 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 3 - Forks: 1

russelllab/wesa

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

Language: HTML - Size: 2.32 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 3 - Forks: 0

pgarrett-scripps/ProteinCleaverStreamlitApp

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

Language: Python - Size: 748 KB - Last synced at: 17 days ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 1

MiguelCos/Fragterminomics

Annotation and processing of peptides from FragPipe search results

Language: R - Size: 42.4 MB - Last synced at: 11 days ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 1

dev-ev/isobaric-inspection-jupyter

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

Language: Jupyter Notebook - Size: 25.1 MB - Last synced at: about 2 months ago - Pushed at: about 3 years ago - Stars: 3 - Forks: 1

SamueldelaCamaraFuentes/TraianProt

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

Language: R - Size: 4.63 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 2 - Forks: 0

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: Python - Size: 726 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 2 - Forks: 0

SamueldelaCamaraFuentes/Downstreaming-analysis-workflow

Pipeline and shiny app for the downstreaming analysis of quantitative proteomic data

Language: R - Size: 8.06 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 2 - Forks: 0

SomaLogic/SomaScan.db

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

Language: R - Size: 5.8 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 2 - Forks: 2

dev-ev/julia-vs-python-ms-scripting

Performance of Julia and Python for reading and matching mass spectrometry data

Language: Jupyter Notebook - Size: 959 KB - Last synced at: about 1 month ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0

dev-ev/isobaric-correlations

Exploring correlations in an isobaric labeling mass spectrometry-based proteomic data set

Language: Jupyter Notebook - Size: 2.9 MB - Last synced at: about 1 month ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 0

symbioticMe/batch_effects_workflow_code

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

Language: R - Size: 12.2 MB - Last synced at: about 1 year ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 2

KacperKaszuba0608/OCIAD1-Analysis

OCIAD1 Analysis

Language: R - Size: 56.2 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 1 - Forks: 0

daisybio/PRONE.Shiny

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

Language: R - Size: 3.32 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

miano-fc/MaxQuant-Tools

Tools for comparing results of two MaxQuant experiments and their respective controls from a run by normalizing data from the output peptides.txt file.

Language: Python - Size: 7.81 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

moritzmadern/InterferenceModeling_in_MultiplexProteomics

Workflow to perform interference modeling and interference correction for MS2-based multiplex proteomics data

Language: R - Size: 44.1 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 1

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: R - Size: 58.5 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 1 - Forks: 3

seerbio/seer-pas-sdk

Python SDK for Seer PAS

Language: Python - Size: 125 KB - Last synced at: 12 months ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

BenBruyneel/proteinDiscover

Provides the ability to read results produced by the Proteome Discoverer software of Thermo Scientific

Language: R - Size: 12.2 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

loankimrobinson/loankimrobinson.github.io

This is Loan Robinson Github Page, which includes all tutorials for education purpose.

Language: HTML - Size: 6.11 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

sivkri/Perseus-MS-Proteomics-Venn

Mass spectrometry Perseus Data analysis

Language: Jupyter Notebook - Size: 330 KB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

bmascat/lfq-proteomics-pipeline

All code, bash scrypts and pipelines used to analyse and visualise proteomic data from my experiments with my first Crispr KO model.

Language: R - Size: 42 KB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

Nino5105/AAI_AKI_multi-omics_code

The R script and relative data set for Integrated single-cell transcriptomics and proteomics reveal cellular-specific response and microenvironment remodeling in aristolochic acid nephropathy

Language: R - Size: 4.6 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

eskutkaan-zz/biodata

a molecular solutions toolbox for molecular biologists.

Language: Python - Size: 65.4 KB - Last synced at: 12 months ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

jessmhoehner/Methods Fork of EmoryIntegratedComputationalCore/Methods

Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.

Language: R - Size: 18 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

uconn-scs/msDiaLogue

Analysis + Visuals for Data Indep. Aquisition Mass Spectrometry Data

Language: R - Size: 73.7 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 0 - Forks: 2

MaayanLab/GeneSetCart

GeneSetCart is an interactive web-based platform that enables investigators to gather gene sets from various sources; augment these sets with gene-gene co-expression correlations and protein-protein interactions; perform set operations on these sets such as union, consensus, and intersection; and visualize and analyze these gene sets.

Language: TypeScript - Size: 17.7 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 0 - Forks: 0

baynec2/mspms

R package for the analysis of Multiplex Substrate Profiling by Mass Spectrometry for Proteases (MSP-MS) Data

Language: R - Size: 53.6 MB - Last synced at: 7 days ago - Pushed at: 17 days ago - Stars: 0 - Forks: 0

borfebor/alpaca_app

GUI based on the alpaca proteomics pipeline for Absolute Protein Quantification data analysis

Language: Python - Size: 16.8 MB - Last synced at: 1 day ago - Pushed at: 27 days ago - Stars: 0 - Forks: 0

borfebor/alpaca_proteomics

Python pipeline for Absolute Protein Quantification data analysis

Language: Jupyter Notebook - Size: 4.03 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

SlavovLab/Protein-Clearance

Analysis from Leduc and Slavov (2025): Protein degradation and growth dependent dilution substantially shape mammalian proteomes

Language: R - Size: 35.2 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

EpistemologistIoneuroscientist/MedicrossSims-GamingCards

1. "A collection of gaming cards for medical simulation and education, combining healthcare expertise with engaging gameplay mechanics."

Size: 2.93 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

SlavovLab/CellPermeability

Cell Permeability analysis

Language: R - Size: 45.9 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

ShilohAlleyne/Bacterial-Efflux-Pump-paring-with-Parser-Combinators

A remake of my BSC research: https://github.com/ShilohAlleyne/Bacterial-Efflux-Pumps-Bioinformatics-Investigations

Language: Haskell - Size: 4.29 MB - Last synced at: 25 days ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

BenBruyneel/proteinDiscoverExtra

Extra (example) functions for using the proteinDiscover R package

Language: R - Size: 46.9 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

Pigrenok/GeneValidator_deploy

This repository describes how GeneValidator can be deployed either using Docker Compose Stack or on AWS ECS stack.

Language: Shell - Size: 12.7 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

lisiarend/PRONE

R Package for preprocessing, normalizing, and analyzing proteomics data

Language: R - Size: 40.4 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

moritzmadern/SiteToProteinNormalization_in_MultiplexProteomics

Workflow to perform unbiased site-to-protein normalization in multiplex proteomics by accounting for ratio compression effects due to ion interference

Language: R - Size: 55.3 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 1

maxperutzlabs-ms/SiteToProteinNormalization_in_MultiplexProteomics Fork of moritzmadern/SiteToProteinNormalization_in_MultiplexProteomics

Workflow to perform unbiased site-to-protein normalization in multiplex proteomics by accounting for ratio compression effects due to ion interference

Language: R - Size: 55.3 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

maxperutzlabs-ms/InterferenceModeling_in_MultiplexProteomics Fork of moritzmadern/InterferenceModeling_in_MultiplexProteomics

Workflow to perform interference modeling and interference correction for MS2-based multiplex proteomics data

Language: R - Size: 44.1 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

cstingl/vrpep-anno

Toolbox and workflow for annotating the variable antibody region of denovo sequenced peptides

Language: Perl - Size: 13 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

radusuciu/yan_etal_natcomm_2024

Code used for processing proteomics data associated with the publication by Yan et al., submitted to Nature Communications in 2024

Language: Python - Size: 13.9 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

BenBruyneel/proteinAnnotation

R Package that enables the display of protein information

Language: R - Size: 92.8 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

baynec2/GLabR

tools for working with proteomics data in the Gonzalez lab

Language: R - Size: 73.6 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

bibs-lab/SpecGlobX

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

Language: Java - Size: 20.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

seanyoon777/proteomics_project

Data analysis on relationship between neurodegenerative diseases and plasma/CSF protein expression levels.

Language: R - Size: 216 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1

chinmayaNK22/PepAnnotate

Generate annotated Peptide Spectrum Matches (PSMs) from proteomic database search result

Language: Python - Size: 16.6 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

chinmayaNK22/DIA-SpecLib_Result_Summarizer

Extract the identified peptides and proteins from spectral library search of DIA proteomic data in Skyline

Language: Python - Size: 35.2 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

chinmayaNK22/R_Scripts

Routinely used R scripts in statistical analysis of proteomic experiment results with figure and plot generation

Language: R - Size: 52.7 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1

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: R - Size: 16.1 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0