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intervene-shiny

An interactive Shiny App for UpSet plots, Venn diagrams and Pairwise heatmaps

kinact

Toolbox for Kinase Activity Scoring based on phosphoproteomic data

liverx

Analysis of liver proteomics data from Aebersold lab

m2aia

Mass spectrometry imaging applications for interactive analysis in MITK (M²aia)

machine-learning-tutorials

machine learning and deep learning tutorials, articles and other resources

massbank-data

Official repository of open data MassBank records

masspix

mayinstitute2020-intermediater

May Institute 2020 Online - Intermediate R Crash Course

metaboanalyst_docker

Docker for MetaboAnalyst 4.0

metaboanalystr

R package for MetaboAnalyst

metaboannotationtutorials

Examples and tutorials for the MetaboAnnotation, MetaboCoreUtils and CompoundDb R packages

metax

metaX: a flexible and comprehensive software for processing metabolomics data.

msexample

An example R package for mass spectrometry

msicompare

*in development* msiCompare is an R package for statistical testing of mass spectrometry imaging data.

msipl

Python Implementation of the msiPL by Abdelmoula et al.

msir

MSIr: Automatic Registration Service for Mass Spectrometry Imaging and Histology

msnbase

Base Classes and Functions for Mass Spectrometry and Proteomics

msstats-shiny

Shiny for MSstats and MSstatsTMT

msstats_labelfree_preprocessing

This repo will contain scripts, sample reports and other resources related to the use of MSstats for preprocessing and normalization of proteomics data

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

normalyzerde

Tools for normalization, evaluation of outliers, technical biases and batch effects and differential expression analysis.

omicsviewer

pacom

PACOM (Proteomics Assay COMparator) is a Java stand alone tool for visualize and compare large proteomics datasets

pdd-shiny

Processing of DIA-NN Data

phantasus

Visual exploratory analysis of gene expression data

pignon

pomashiny

:apple: Web-based User-friendly Workflow for Metabolomics and Proteomics Data Analysis

programmingassignment2

Repository for Programming Assignment 2 for R Programming on Coursera

protein-coverage-summarizer

Computes the percent of the residues in each protein sequence that have been identified, based on a list of identified peptides. A graphical user interface (GUI) is provided to allow the user to select the input files, set the options, and browse the coverage results.

pydiaid

An open-source Python package for dia-PASEF methods with Automated Isolation Design (py_diAID) from the Mann Labs at the Max Planck Institute of Biochemistry.