rawrr - 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

8.70 score 61 stars 3 dependents 41 scripts 535 downloads

protViz - 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

7.88 score 11 stars 2 dependents 72 scripts 386 downloads

rawDiag - 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

6.23 score 37 stars 23 scripts 252 downloads

recmap - 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

5.85 score 23 stars 31 scripts 515 downloads

MsBackendRawFileReader - 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

5.73 score 6 stars 12 scripts 340 downloads

specL - 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

5.42 score 1 stars 11 scripts 406 downloads

cloudUtil - Cloud Utilization Plots

Provides means of plots for comparing utilization data of compute systems.

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2.00 score 4 scripts 187 downloads