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MALDIquant - Quantitative Analysis of Mass Spectrometry Data

A complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.

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7.31 score 52 dependents 227 scripts 5.8k downloads

cleaver - Cleavage of Polypeptide Sequences

In-silico cleavage of polypeptide sequences. The cleavage rules are taken from: http://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html

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proteomics

5.84 score 2 dependents 38 scripts 787 downloads

topdownr - Investigation of Fragmentation Conditions in Top-Down Proteomics

The topdownr package allows automatic and systemic investigation of fragment conditions. It creates Thermo Orbitrap Fusion Lumos method files to test hundreds of fragmentation conditions. Additionally it provides functions to analyse and process the generated MS data and determine the best conditions to maximise overall fragment coverage.

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immunooncologyinfrastructureproteomicsmassspectrometrycoverage

5.32 score 1 dependents 507 downloads

zlog - Z(log) Transformation for Laboratory Measurements

Transformation of laboratory measurements into z or z(log)-value based on given or empirical reference limits as proposed in Hoffmann et al. 2017 <doi:10.1515/labmed-2016-0087>.

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laboratory-measurementstransformationzlog

4.00 score 2 stars 225 downloads

readMzXmlData - Reads Mass Spectrometry Data in mzXML Format

Functions for reading mass spectrometry data in mzXML format.

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3.93 score 3 dependents 19 scripts 682 downloads

MALDIquantForeign - Import/Export Routines for 'MALDIquant'

Functions for reading (tab, csv, Bruker fid, Ciphergen XML, mzXML, mzML, imzML, Analyze 7.5, CDF, mMass MSD) and writing (tab, csv, mMass MSD, mzML, imzML) different file formats of mass spectrometry data into/from 'MALDIquant' objects.

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3.85 score 71 scripts 634 downloads

topdownrdata - Example Files for the topdownr R Package

Example data for the topdownr package generated on a Thermo Orbitrap Fusion Lumos MS device.

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experimentdatamassspectrometrydatadatapkg

3.18 score

readBrukerFlexData - Reads Mass Spectrometry Data in Bruker *flex Format

Reads data files acquired by Bruker Daltonics' matrix-assisted laser desorption/ionization-time-of-flight mass spectrometer of the *flex series.

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1.78 score 1 stars 2 dependents 10 scripts 510 downloads