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Projects in Awesome Lists tagged with mass-spectrometry

A curated list of projects in awesome lists tagged with mass-spectrometry .

https://github.com/lazear/sage

Proteomics search & quantification so fast that it feels like magic

bioinformatics mass-spectrometry proteomics

Last synced: 12 Nov 2024

https://github.com/sneumann/xcms

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis

bioconductor feature-detection mass-spectrometry metabolomics peak-detection r

Last synced: 19 Dec 2024

https://github.com/bittremieux/spectrum_utils

Python package for efficient mass spectrometry data processing and visualization

mass-spectrometry

Last synced: 15 Dec 2024

https://github.com/lgatto/msnbase

Base Classes and Functions for Mass Spectrometry and Proteomics

bioconductor bioinformatics mass-spectrometry proteomics proteomics-data r visualisation

Last synced: 20 Dec 2024

https://github.com/lgatto/MSnbase

Base Classes and Functions for Mass Spectrometry and Proteomics

bioconductor bioinformatics mass-spectrometry proteomics proteomics-data r visualisation

Last synced: 12 Nov 2024

https://github.com/Nesvilab/philosopher

PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering

bioinformatics data-analysis go mass-spectrometry ms-data proteomics

Last synced: 09 Nov 2024

https://github.com/lgatto/rforproteomics

Using R and Bioconductor packages for the analysis and comprehension of proteomics data.

bioconductor bioconductor-packages mass-spectrometry proteomics proteomics-data r tutorial

Last synced: 27 Oct 2024

https://github.com/wfondrie/depthcharge

A deep learning toolkit for mass spectrometry

deep-learning framework mass-spectrometry metabolomics proteomics pytorch

Last synced: 21 Dec 2024

https://github.com/sgibb/maldiquant

Quantitative Analysis of Mass Spectrometry Data

cran maldi maldi-ims maldi-tof-ms mass-spectrometry r r-package

Last synced: 16 Dec 2024

https://github.com/rickhelmus/patRoon

Workflow solutions for mass-spectrometry based non-target analysis.

mass-spectrometry non-target r

Last synced: 04 Dec 2024

https://github.com/cgohlke/molmass

Molecular mass calculations

chemistry mass-spectrometry python

Last synced: 11 Nov 2024

https://github.com/fgcz/rawrr

Access Orbitrap data in R lang using C# mono assembly - bioconductor package

fast mass-spectrometry multiplatform orbitrap-ms rpackage

Last synced: 15 Dec 2024

https://github.com/ursgal/ursgal

Ursgal - universal Python module combining common bottom-up proteomics tools for large-scale analysis

mass-spectrometry ms-data mzml omics peptide-identification proteomics proteomics-data python

Last synced: 12 Nov 2024

https://github.com/rformassspectrometry/spectra

Low level infrastructure to handle MS spectra

bioconductor mass-spectrometry metabolomics proteomics rstats

Last synced: 20 Dec 2024

https://rformassspectrometry.github.io/Spectra/

Low level infrastructure to handle MS spectra

bioconductor mass-spectrometry metabolomics proteomics rstats

Last synced: 07 Nov 2024

https://github.com/fgcz/rawDiag

Brings Orbitrap mass spectrometry data to life; multi-platform, fast and colorful R package

fast mass-spectrometry multiplatform orbitrap r rpackage visualization

Last synced: 12 Nov 2024

https://github.com/fgcz/rawdiag

Brings Orbitrap mass spectrometry data to life; multi-platform, fast and colorful R package

fast mass-spectrometry multiplatform orbitrap r rpackage visualization

Last synced: 15 Dec 2024

https://github.com/lkytal/pepnet

The state of the art Deep CNN neural network for de novo sequencing of tandem mass spectra

convolutional-neural-networks deep-learning mass-spectrometry

Last synced: 12 Nov 2024

https://github.com/chasemc/IDBacApp

A MALDI Mass Spectrometry Bioinformatics Platform

mass-spectrometry microbiology r shiny

Last synced: 04 Dec 2024

https://github.com/metgem/metgem

Calculation and visualization of molecular networks based on t-SNE algorithm

chemistry chemoinformatics cosine-similarity graph mass-spectrometry metabolomics network networking

Last synced: 07 Nov 2024

https://github.com/chasemc/idbacapp

A MALDI Mass Spectrometry Bioinformatics Platform

mass-spectrometry microbiology r shiny

Last synced: 27 Oct 2024

https://github.com/lkytal/predfull

This work was published on Analytical Chemistry: Full-Spectrum Prediction of Peptides Tandem Mass Spectra using Deep Neural Network

mass-spectrometry peptides spectrum tensorflow

Last synced: 12 Nov 2024

https://github.com/bittremieux/falcon

Large-scale tandem mass spectrum clustering using fast nearest neighbor searching.

clustering mass-spectrometry nearest-neighbor-search

Last synced: 17 Nov 2024

https://github.com/Vitek-Lab/MSstatsTMT

R-based package for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

labeling mass-spectrometry msstats proteomics tmt tmt-data-analysis

Last synced: 12 Nov 2024

https://github.com/rformassspectrometry/qfeatures

Quantitative features for mass spectrometry data

bioconductor mass-spectrometry metabolomics proteomics rstats

Last synced: 16 Dec 2024

https://rformassspectrometry.github.io/QFeatures/

Quantitative features for mass spectrometry data

bioconductor mass-spectrometry metabolomics proteomics rstats

Last synced: 07 Nov 2024

https://github.com/pwilmart/tmt_analysis_examples

Examples of TMT data analyses using R. Links to notebooks and repositories. Also a few spectral counting analyses.

ipynb jupyter-notebook mass-spectrometry proteomics proteomics-data r tmt tmt-data-analyses

Last synced: 11 Oct 2024

https://github.com/snijderlab/stitch

Template-based assembly of proteomics short reads for de novo antibody sequencing and repertoire profiling

antibody mass-spectrometry sequencing

Last synced: 22 Nov 2024

https://github.com/domdfcoding/pynist

PyMassSpec extension for searching mass spectra using NIST's Mass Spectrum Search Engine.

c chemistry mass-spectrometry python python3

Last synced: 18 Dec 2024

https://github.com/molecularcartography/optimus

Workflow for LC-MS feature analysis and spatial mapping

knime lc-ms mass-spectrometry metabolomics python27 sqlite3 workflow

Last synced: 10 Nov 2024

https://github.com/rformassspectrometry/compounddb

Creating and using (chemical) compound databases

annotation databases mass-spectrometry metabolomics rstats

Last synced: 16 Dec 2024

https://github.com/pwilmart/irs_normalization

An exploration of internal reference scaling (IRS) normalization in isobaric tagging proteomics experiments.

ipynb irs-normalization jupyter-notebook mass-spectrometry normalization proteomics proteomics-data r tmt

Last synced: 11 Oct 2024

https://github.com/yufree/envigcms

GC/LC-MS data analysis for environmental science

cran environment mass-spectrometry metabolomics r

Last synced: 27 Oct 2024

https://github.com/bittremieux/gleams

GLEAMS is a Learned Embedding for Annotating Mass Spectra.

clustering deep-learning mass-spectrometry

Last synced: 27 Oct 2024

https://github.com/idslme/idsl.ipa

Intrinsic Peak Analysis (IPA) pipeline for peak-picking in large-scale untargeted small molecule analysis including metabolomics, lipidomics, exposomics, and environmental studies.

cran exposome feature-detection lipidomics mass-spectrometry metabolomics peak-detection peak-picking r small-molecule untargeted-metabolomics

Last synced: 17 Nov 2024

https://github.com/cpanse/protviz

Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

cran fun mass-spectrometry peptide-identification proteomics quantification rstats visualization

Last synced: 15 Dec 2024

https://github.com/rformassspectrometry/rformassspectrometry.org

The R for Mass Spectrometry Initiative home page

bioconductor mass-spectrometry rstats

Last synced: 16 Nov 2024

https://github.com/josiehong/3dmolms

[Bioinformatics] 3DMolMS: prediction of tandem mass spectra from 3D molecular conformations

mass-spectrometry molecule

Last synced: 09 Oct 2024

https://github.com/ipb-halle/metfamily

Understanding metabolism is fundamental in biomedical and plant research and the identification and quantification of thousands of metabolites by mass spectrometry in modern metabolomics is a prerequisite for elucidating this area. However, the identification of metabolites is a major bottleneck in traditional approaches hampering advances. Here, we present a novel approach for the untargeted discovery of metabolite families offering a bird's eye view of metabolic regulation in comparative metabolomics. We implemented the presented methodology in the easy-to-use web application MetFamily to enable the analysis of comprehensive metabolomics studies for all researchers worldwide. MetFamily is available under http://msbi.ipb-halle.de/MetFamily/.

analysis annotation comprehensive-metabolomics-studies mass-spectrometry metabolites

Last synced: 10 Dec 2024

https://github.com/bigbio/py-pgatk

Python tools for proteogenomics analysis toolkit

ensembl mass-spectrometry proteogenomics proteogenomics-analysis-toolkit proteomics python vcf

Last synced: 28 Nov 2024

https://github.com/sgibb/maldiquantforeign

Import/Export routines for MALDIquant

csv export import maldi mass-spectrometry msd-files mzml r

Last synced: 27 Oct 2024

https://github.com/yufree/pmd

Paired Mass Distance(PMD) analysis for GC/LC-MS based nontarget analysis

mass-spectrometry metabolomics non-target

Last synced: 27 Oct 2024

https://github.com/fgcz/bfabricshiny

Manage life sciences data using R and b-fabric - a WSDL/REST interface and a tool box; main focus on MS data

bfabric experiments mass-spectrometry omics shiny wsdl

Last synced: 15 Dec 2024

https://github.com/pgarrett-scripps/peptacular

A spectacularly simple package for working with peptide sequences.

bioinformatics mass-spectrometry peptide-identification peptide-sequences peptides protein proteomics python

Last synced: 05 Dec 2024

https://github.com/rformassspectrometry/spectripy

Interfacing R's Spectra package with the Python world.

infrastructure mass-spectrometry python rstats

Last synced: 16 Nov 2024

https://github.com/rformassspectrometry/book

R for Mass Spectrometry documentation

documentation mass-spectrometry metabolomics proteomics

Last synced: 16 Nov 2024

https://github.com/rformassspectrometry/metabocoreutils

Core utilities for metabolomics.

mass-spectrometry metabolomics

Last synced: 16 Nov 2024

https://github.com/rformassspectrometry/protgenerics

S4 generic functions for Bioconductor mass spectrometry infrastructure

bioconductor mass-spectrometry metabolomics proteomics r

Last synced: 12 Oct 2024

https://github.com/jorainer/metaboannotationtutorials

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

annotation mass-spectrometry metabolomics

Last synced: 19 Nov 2024

https://github.com/rformassspectrometry/msbackendtimstof

Spectra backend supporting TimsTOF data files using the opentimsr package.

infrastructure mass-spectrometry rstats

Last synced: 16 Nov 2024

https://github.com/rformassspectrometry/unimod

Amino acid modifications for mass spectrometry

amino-acid-modifications mass-spectrometry protein proteomics r

Last synced: 16 Nov 2024

https://github.com/idslme/idsl.mxp

A light weight and fast parser for reading mzML, mzXML and netCDF data files

exposome gc-ms-data lc-ms-data lipidomics mass-spectrometry metabolomics mzml mzxml netcdf r

Last synced: 09 Nov 2024

https://github.com/dev-ev/ms-interactive-viz

Customizable and informative mass spectra with Bokeh

bokeh interactive-visualizations mass-spectrometry proteomics visualization

Last synced: 19 Nov 2024

https://github.com/barupal/adni

Alzheimer's Disease Neuroimaging Initiative: Untargeted Lipidomics Analysis

adni alzheimers-disease lcms lipidomics mass-spectrometry metabolomics

Last synced: 17 Nov 2024

https://github.com/cpanse/nestlink

Engineered Peptide Barcodes for In-Depth Analyses of Binding Protein Ensembles - replication code

bioconductor mass-spectrometry prediction retention-time rpackage sequencing simulation

Last synced: 15 Dec 2024

https://github.com/lgatto/rpx

R Interface to the ProteomeXchange Repository

bioconductor data mass-spectrometry proteomexchange proteomics

Last synced: 28 Oct 2024

https://github.com/rformassspectrometry/msbackendmsp

Mass Spectrometry Data Backend for MSP Files

infrastructure mass-spectrometry rstats

Last synced: 16 Nov 2024

https://github.com/pgarrett-scripps/fastaframes

Python package to convert between FASTA files and Pandas DataFrames.

bioinformatics fasta mass-spectrometry package pandas protein protein-sequences proteomics python

Last synced: 05 Dec 2024

https://github.com/molecularcartography/optimusviewer

An app for visualizing LC-MS features detected with Optimus workflow

amcharts cplusplus-11 data-visualization javascript lc-ms mass-spectrometry qt5 sqlite3

Last synced: 10 Nov 2024

https://github.com/tnaake/metcirc

GitHub repository for MetCirc. The development version in Bioconductor can be found at:

mass-spectrometry metabolomics metabolomics-pipeline r visualization

Last synced: 24 Nov 2024

https://github.com/utrechtuniversity/clumped-processing

Clumped isotope measurement processing script for Thermo Fisher MAT 253 plus isotope ratio mass spectrometer with the Kiel IV

clumped clumped-isotopes isotope mass-spectrometry stable-isotopes

Last synced: 22 Nov 2024

https://github.com/jamesetsmith/msanalysis

Python Tools for Mass Spec. Analysis

mass-spectrometry matplotlib mzxml python scipy

Last synced: 31 Oct 2024

https://github.com/metgem/libmetgem

A library for molecular networking based on MS/MS spectra.

chemistry chemoinformatics cosine-similarity cython mass-spectrometry

Last synced: 07 Nov 2024

https://github.com/dev-ev/isobaric-inspection-jupyter

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

data-quality data-visualization data-wrangling isobaric-labeling jupyterlab mass-spectrometry proteome-discoverer proteomics proteomics-data-analysis python quantitative-proteomics

Last synced: 19 Nov 2024

https://github.com/idslme/ccdb

Chemical Correlation Database (CCDB)

exposome mass-spectrometry metabolomics

Last synced: 17 Nov 2024

https://github.com/mdeff/srfsp

Super-resolution for mass spectrometry

mass-spectrometry signal-processing super-resolution

Last synced: 21 Nov 2024

https://github.com/m-jahn/R-tools

often used R scripts for bio-informatics work and plotting

goterm helper-functions mass-spectrometry proteomics r-programming

Last synced: 04 Dec 2024

https://github.com/dev-ev/julia-vs-python-ms-scripting

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

benchmarking julia mass-spectrometry numpy performance-testing proteomics-data-analysis python

Last synced: 19 Nov 2024

https://github.com/zanpeeters/quicklooksims

QuickLook and Spotlight plugins for SIMS files.

mass-spectrometry quicklook science sims spotlight

Last synced: 12 Dec 2024

https://github.com/zanpeeters/interference_calculator

Calculate mass interference based on the composition of a sample and a target.

mass-spectrometry science sims

Last synced: 21 Dec 2024

https://github.com/rformassspectrometry/msbackendmetabolights

MsBackend allowing to retrieve MS data from the MetaboLights repository.

mass-spectrometry metabolomics metabolomics-data

Last synced: 16 Nov 2024

https://github.com/rformassspectrometry/msio

Serializing/importing mass spectrometry data objects eventually using language-agnostic formats.

mass-spectrometry metabolomics proteomics

Last synced: 16 Nov 2024

https://github.com/michaelwitting/metabolomicsutils

This repository contains several utility functions for MS based metabolomics

mass-spectrometry metabolite-identification metabolomics

Last synced: 16 Nov 2024

https://github.com/dev-ev/protexam

Inspect your quantitative proteomics results using this streamlit-powered dashboard. The dashboard is specifically tailored for the comprehensive examination of the result of isobaric labeling-based quantitative proteomics.

mass-spectrometry proteomics streamlit streamlit-webapp visualization

Last synced: 09 Nov 2024

https://github.com/domdfcoding/pywine-pyms-nist

Docker image for the Flask search server for PyMassSpec NIST Search

chemistry docker flask mass-spectrometry python3

Last synced: 06 Dec 2024

https://github.com/maxozo/plf

Peptide location fingerprinting (PLF) is a technique capable of identifying modified proteins and potential causal mechanisms in complex biological samples. Protein Locational Fingerprinter determines statisticaly significant peptide yields from protein functional domains.

domains mass-spectrometry proteomics

Last synced: 28 Nov 2024

https://github.com/ralfg/pyrawr

Python wrapper around the ThermoRawFileParser command line interface.

mass-spectrometry proteomics raw thermorawfileparser

Last synced: 14 Dec 2024

https://github.com/domdfcoding/msp2lib

Convert an MSP file representing one or more Mass Spectra to a NIST MS Search user library.

chemistry docker mass-spectrometry python python3 wine

Last synced: 18 Oct 2024

https://github.com/juliomarcopineda/peptide-serum-stability

Analyze possible peptide fragments with peptide serum stability studies.

cyclic-peptides java mass-spectrometry peptide-fragments peptide-serum-stability peptides stability

Last synced: 11 Nov 2024