A mass spectrometry package for Julia
This package is unregistered. It can be installed either with the Julia package manager.
From the Julia REPL, type ]
to enter the Pkg REPL mode and run:
(v1.3) pkg> add https://github.com/ajgiuliani/MSj.jl
or using the package API:
using Pkg
Pkg.add(PackageSpec(url="https://github.com/ajgiuliani/MSj.jl"))
Documentation is available here.
MSj is a package for loading, processing and plotting mass spectrometry data. It provides the following functionalities:
Getting information on the file
Load a file
Averaging mass spectra based on various criteria that may be combined
Chromatogram and extracted chromatograms
Processing the data
smoothing
baseline correction
peak-picking
Calculation of isotopic distribution
To get information on a file:
info("path/to/file")
Mass spectra can be loaded by:
data = load("path/to/file")
And averaged as follow:
ms1 = average(data, MSj.Level(1)) # full MS scans
ms2 = average(data, MSj.Level(2)) # MS2 spectra
ms3 = average(data, MSj.Activation_Method("CID")) # CID spectra
See the documentation for additional information.
- mzxml
- mzXML.jl: Load mass spectrometry mzXML files.
- MassSpec.jl: Mass spectometry utilities for Julia