rawrr - Direct Access to Orbitrap Data and Beyond
This package wraps the functionality of the RawFileReader .NET 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.
Last updated 16 days ago
massspectrometryproteomicsmetabolomicsinfrastructuresoftware
52 stars 3.58 score 0 dependencies 2 dependentsrawDiag - 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.
Last updated 12 days ago
massspectrometryproteomicsmetabolomicsinfrastructuresoftwareshinyapps
36 stars 3.19 score 70 dependenciesprotViz - 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.
Last updated 9 months ago
funmass-spectrometrypeptide-identificationproteomicsquantificationvisualization
11 stars 2.51 score 1 dependencies 2 dependentsrecmap - 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., different countries, is represented by a rectangle. The area of each rectangle represents the statistical value given as input (maintain zero cartographic error). C++ is used to implement the computationally intensive tasks. The vignette included in this package provides documentation about the usage of the recmap algorithm.
Last updated 9 months ago
cartogramdemographicsgenetic-algorithmgeovisualizationgraph-drawingspatialspatial-data-analysisvalue-by-area-maps
20 stars 2.24 score 10 dependenciesMsBackendRawFileReader - 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.
Last updated 16 days ago
massspectrometryproteomicsmetabolomics
4 stars 1.51 score 22 dependenciesspecL - 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>.
Last updated 4 months ago
massspectrometryproteomics
1 stars 1.45 score 27 dependenciescloudUtil - Cloud Utilization Plots
Provides means of plots for comparing utilization data of compute systems.
Last updated 8 years ago
0.00 score 0 dependencies