prolfqua - Proteomics Label Free Quantification
The prolfqua package integrates essential steps of the mass spectrometry based label free quantification data analysis workflow: quality control, data normalization, protein aggregation, modeling, hypothesis testing and sample size estimation. We use prolfqua to : develop highly customizable, visually appealing, and interactive data analysis reports in pdf or HTML format; to visualize and model simple experimental designs with a single explanatory variable and complex experiments with multiple factors; to benchmark data acquisition, data preprocessing or data modeling methods. We developed and improved the package by applying the "Eating your own dog food" principle, when analysing dozens of proteomics datasets.
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massspectrometryproteomicsmetabolomicsnormalizationpreprocessingqualitycontroldifferential-expression-analysishypothesis-testingprotein-quantificationproteomics-data-analysisquality-control
8.38 score 48 stars 44 scripts 50 downloadsprotViz - Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics
Helps with quality checks, visualizations and analysis of mass spectrometry data, coming from proteomics experiments. The package is developed, tested and used at the Functional Genomics Center Zurich <https://fgcz.ch>. We use this package mainly for prototyping, teaching, and having fun with proteomics data. But it can also be used to do data analysis for small scale data sets.
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funmass-spectrometrypeptide-identificationproteomicsquantificationvisualizationcpp
8.17 score 11 stars 3 dependents 93 scripts 519 downloadsrawrr - Direct Access to Orbitrap Data and Beyond
This package wraps the functionality of the Thermo Fisher Scientic RawFileReader .NET 8.0 assembly. Within the R environment, spectra and chromatograms are represented by S3 objects. The package provides basic functions to download and install the required third-party libraries. The package is developed, tested, and used at the Functional Genomics Center Zurich, Switzerland.
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massspectrometryproteomicsmetabolomicsinfrastructuresoftwarefastmass-spectrometrymultiplatformorbitrap-ms
8.11 score 62 stars 2 dependents 70 scripts 480 downloadsrawDiag - Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful
Optimizing methods for liquid chromatography coupled to mass spectrometry (LC-MS) poses a nontrivial challenge. The rawDiag package facilitates rational method optimization by generating MS operator-tailored diagnostic plots of scan-level metadata. The package is designed for use on the R shell or as a Shiny application on the Orbitrap instrument PC.
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massspectrometryproteomicsmetabolomicsinfrastructuresoftwareshinyappsfastmass-spectrometrymultiplatformorbitrapvisualization
6.03 score 37 stars 29 scripts 338 downloadsMsBackendRawFileReader - Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files
implements a MsBackend for the Spectra package using Thermo Fisher Scientific's NewRawFileReader .Net libraries. The package is generalizing the functionality introduced by the rawrr package Methods defined in this package are supposed to extend the Spectra Bioconductor package.
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massspectrometryproteomicsmetabolomics
5.78 score 6 stars 20 scripts 458 downloadsspecL - specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
provides a functions for generating spectra libraries that can be used for MRM SRM MS workflows in proteomics. The package provides a BiblioSpec reader, a function which can add the protein information using a FASTA formatted amino acid file, and an export method for using the created library in the Spectronaut software. The package is developed, tested and used at the Functional Genomics Center Zurich <https://fgcz.ch>.
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massspectrometryproteomicsddadiamass-spectrometry
5.64 score 1 stars 18 scripts 614 downloadsrecmap - Compute the Rectangular Statistical Cartogram
Implements the RecMap MP2 construction heuristic (<doi:10.1109/INFVIS.2004.57>). This algorithm draws maps according to a given statistical value (e.g., election results, population, or epidemiological data). The basic idea of the RecMap algorithm is that each map region (e.g., a country) is represented by a rectangle whose area reflects the provided statistical value, thereby maintaining zero cartographic error. Computationally intensive tasks are implemented in C++. The included vignette documents usage of the recmap algorithm.
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cartogramdemographicsgenetic-algorithmgeovisualizationgraph-drawingspatialspatial-data-analysisvalue-by-area-mapscpp
5.58 score 23 stars 33 scripts 536 downloadsmsqc1 - Sigma mix MSQC1 data
contains eight technical replicate data set and a three replicate dilution series of the MS Qual/Quant Quality Control Mix standard sample (Sigma-Aldrich, Buchs, Switzerland) measured on five different mass spectrometer platforms at the Functional Genomics Center Zurich.
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experimentdatamassspectrometrydatareproducibleresearchdatapkg
4.48 score 10 scriptstartare - Raw ground spectra recorded on Thermo Fisher Scientific mass spectrometers
Provides raw files recorded on different Liquid Chromatography Mass Spectrometry (LC-MS) instruments. All included MS instruments are manufactured by Thermo Fisher Scientific and belong to the Orbitrap Tribrid or Q Exactive Orbitrap family of instruments. Despite their common origin and shared hardware components, e.g., Orbitrap mass analyser, the above instruments tend to write data in different "dialects" in a shared binary file format (.raw). The intention behind tartare is to provide complex but slim real-world files that can be used to make code robust with respect to this diversity. In other words, it is intended for enhanced unit testing. The package is considered to be used with the rawrr package and the Spectra MsBackends.
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experimentdatamassspectrometrydataexperimenthubbioconductorblobdataunittestingdatapkg
4.00 score 1 stars 2 scriptscloudUtil - Cloud Utilization Plots
Provides means of plots for comparing utilization data of compute systems.
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2.00 score 4 scripts 288 downloads