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Search results for mass spectrometry
mass-spectrometry
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181 search results found
Msbuddy
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11
a python package for molecular formula analysis in MS-based small molecule studies
Metaboigniter
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11
Pre-processing of mass spectrometry-based metabolomics data with quantification and identification based on MS1 and MS2 data.
Stitch
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11
Template-based assembly of proteomics short reads for de novo antibody sequencing and repertoire profiling
Dart Id
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10
DART-ID: retention time alignment and peptide identification confidence updates
Denovopipeline
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10
Pipeline for de novo peptide sequencing (Novor, DeepNovo, SMSNet, PointNovo, Casanovo) and assembly with ALPS.
Rformassspectrometry.org
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10
The R for Mass Spectrometry Initiative home page
Pointiso
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9
This is the implementation of PointIso model presented in the paper "Deep neural network for detecting arbitrary precision peptide features through attention based segmentation" (https://www.nature.com/articles/s41598-021-97669- and https://arxiv.org/abs/2009.07250). For any inquiry about running the codes, contact me (Fatema):
[email protected]
Maldiquantforeign
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9
Import/Export routines for MALDIquant
Beamspy
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9
BEAMSpy - Birmingham mEtabolite Annotation for Mass Spectrometry (Python Package)
Protviz
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9
Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics
Goslin
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9
Goslin is the Grammar on succinct lipid nomenclature.
Irs_normalization
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9
An exploration of internal reference scaling (IRS) normalization in isobaric tagging proteomics experiments.
Sdk
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9
Software solution for common top-down proteomics tasks
Promor
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9
A comprehensive R package for label-free proteomics data analysis and modeling
Quantms
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9
Quantitative mass spectrometry workflow.
Protein Contaminant Libraries For Dda And Dia Proteomics
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9
This project is created by the Hao Lab at the Chemistry Department in George Washington University, Washington, D.C..(Publication pending) This project aims to provide contaminant protein FASTA and spectral libraries that can be universally applied to DDA and DIA proteomics and freely accessible for the proteomics community.
Pridepy
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9
Python client for PRIDE Archive Rest API.
Bfabricshiny
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8
Manage life sciences data using R and b-fabric - a WSDL/REST interface and a tool box; main focus on MS data
Quantable
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8
Streamlines descriptive analysis of quantitative mass spectrometry data.
Mzdata
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8
Tripoli
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8
Tripoli imports raw mass spectrometer data files and supports interactive review and archiving of isotopic data. Tripoli facilitates visualization of temporal trends and scatter during measurement, statistically rigorous filtering of data, and calculation of statistical parameters.
Mspypeline
⭐
8
Package to analyze Mass Spec Data
Ionmob
⭐
8
An open-source prediction framework for peptide ion collision cross section (CCS) values with python.
Npdtools
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8
Natural Product Discovery tools -- a toolkit containing various pipelines for in silico analysis of natural product mass spectrometry data
Specter
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8
Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics
Tmt_analysis_examples
⭐
7
Examples of TMT data analyses using R. Links to notebooks and repositories. Also a few spectral counting analyses.
Pymass
⭐
7
Package for analyzing MS with Python
Prospect
⭐
7
Proteomics Mass Spectrometry Datasets for Machine Learning
Pmd
⭐
7
Paired Mass Distance(PMD) analysis for GC/LC-MS based nontarget analysis
Lobstahs
⭐
7
Git repository for the R package "LOBSTAHS" (Lipid and Oxylipin Biomarker Screening Through Adduct Hierarchy Sequences)
Cyclobranch
⭐
7
A tool for mass spectrometry data analysis.
Plexdia
⭐
7
Multiplexed data-independent acquisition (plexDIA) for increasing proteomics throughput. The code is distributed by an MIT license.
Plotms
⭐
7
Plot program for QCxMS spectrum plotting
Book
⭐
7
R for Mass Spectrometry documentation
Rustyms
⭐
7
A rust library for parsing Pro Forma peptides and matching them against MS spectra
Metfamily
⭐
7
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 metab
Candycrunch
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7
Predicting glycan structure from LC-MS/MS data
3dmolms
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7
3DMolMS: prediction of tandem mass spectra from 3D molecular conformations
Metabocoreutils
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7
Core utilities for metabolomics.
Ms File Info Scanner
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7
Examines a series of MS data files (or data directories) and extracts the acquisition start and end times, number of spectra, and the total size of the data. In addition, it can create 2D-plot graphics of the m/z values vs. time for QA purposes.
Metabcombiner
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6
metabCombiner R Package: Paired Untargeted Metabolomics Feature Matching & Data Concatenation
Sm Engine
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6
Engine for metabolite annotation for imaging mass spectrometry
Avant_garde
⭐
6
Avant-garde (AvG) is a new tool to refine Data-Independent Acquisition (and Parallel Reaction Monitoring) by removing interfered transitions, adjusting integration boundaries and scoring peaks to control the FDR.
Lcms Spectator
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6
LCMS raw data and MS-GF+ results viewer
Metaboannotationtutorials
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6
Examples and tutorials for the MetaboAnnotation, MetaboCoreUtils and CompoundDb R packages
Reproduciblemsguidelines
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6
This project aims at defining a set of guidelines for reproducible mass spectrometry-based experiments.
Mass Suite
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6
Mzrecal
⭐
6
Recalibrate Mass Spectrometry data in mzML format
Dimspy
⭐
6
Python package for processing direct-infusion mass spectrometry-based metabolomics and lipidomics data
Py Pgatk
⭐
6
Python tools for proteogenomics analysis toolkit
Msj.jl
⭐
6
A mass spectrometry package for Julia
Autoccs
⭐
6
Automated Collision Cross Section calculation software for ion mobility spectrometry-mass spectrometry
Pimz
⭐
6
This framework allows to perform scRNA-seq-like analyses of imaging mass-spectrometry data. Check out the example jupyter-notebook in examples/
Msquality
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6
Msviz Backend
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6
A mass spectrometry visualization platform, developed by the PAF & Vital-IT, Swiss Institute of Bioinformatics.
Msstatsconvert
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6
Converter functions for the MSstats package
Lipidhunter
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6
LipidHunter is capable to perform bottom up identification of lipids from LC-MS/MS and shotgun lipidomics data by resembling a workflow of manual spectra annotation. LipidHunter generates interactive HTML output with its unique six-panel-image, which provides an easy way to review, store, and share the identification results.
Rmwf
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6
Reproducilble Metabolomics Workflow
Hadex
⭐
6
Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data
Molecular Weight Calculator Dll
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6
The Molecular Weight Calculator can be used to calculate the molecular weight and percent composition of chemical formulas and amino acids (peptides). It includes several other utility modules and is available as both a GUI version and a C# DLL version.
Rapid Qc Ms
⭐
5
Realtime quality control for mass spectrometry data acquisition
Msbackendtimstof
⭐
5
Spectra backend supporting TimsTOF data files using the opentimsr package.
Unimod
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5
Amino acid modifications for mass spectrometry
Protein Coverage Summarizer
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5
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.
Pepfoot
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5
PepFoot: a user friendly GUI for protein footprinting analysis
Idsl.ufa
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5
United Formula Annotation (UFA) for LC-HRMS data
Rump
⭐
5
A Reproducible Untargeted Metabolomics Data Processing Pipeline
Peptacular
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5
A spectacularly simple package for working with peptide sequences.
Untargeted_metabolomics_workflow
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5
Collaborative workflow for untargeted metabolomics data processing and analysis using open-source tools. https://doi.org/10.3390/metabo13040463
Staver
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5
A Standardized Dataset-Based Algorithm for Efficient Variation Reduction in Large-Scale DIA MS Data.
Origami
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5
Software suite for analysis of activated ion mobility mass spectrometry data
Cosims
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5
CoSIMS, a Collision Simulator for Ion Mobility Spectrometry
Synthedia
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5
Create synthetic DIA LC-MS/MS for proteomics experiments
Protgenerics
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5
S4 generic functions for Bioconductor mass spectrometry infrastructure
Msmetaenhancer
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5
Tool for mass spectra metadata annotation.
Physiofit
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5
Estimation of extracellular fluxes and growth rate
Msread
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5
Read popular mass spectrometry formats
Mzid To Tsv Converter
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5
Converts an mzIdentML created by MS-GF+ to a tab-delimited text file.
Massdash
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5
MassDash: A web-based dashboard for streamlined DIA-MS visualization, analysis, prototyping, and optimization
Rptmvalidation
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5
Validation of rare PTM obtained from mass spectrometry-based shotgun proteomics.
Spectripy
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5
Interfacing R's Spectra package with the Python world.
101-181 of 181 search results
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