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.

Last updated 3 months ago

massspectrometryproteomicsmetabolomicsinfrastructuresoftwarefastmass-spectrometrymultiplatformorbitrap-ms

8.19 score 56 stars 2 dependents 23 scripts 406 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.

Last updated 1 years ago

funmass-spectrometrypeptide-identificationproteomicsquantificationvisualizationcpp

7.88 score 11 stars 2 dependents 72 scripts 811 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.

Last updated 4 months ago

massspectrometryproteomicsmetabolomicsinfrastructuresoftwareshinyappsfastmass-spectrometrymultiplatformorbitrapvisualization

6.81 score 36 stars 18 scripts 152 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.

Last updated 4 months ago

massspectrometryproteomicsmetabolomics

5.94 score 5 stars 5 scripts 216 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., 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 2 months ago

cartogramdemographicsgenetic-algorithmgeovisualizationgraph-drawingspatialspatial-data-analysisvalue-by-area-mapscpp

5.51 score 21 stars 31 scripts 430 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>.

Last updated 5 months ago

massspectrometryproteomicsddadiamass-spectrometry

5.46 score 1 stars 12 scripts 280 downloads

cloudUtil - Cloud Utilization Plots

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

Last updated 9 years ago

2.00 score 4 scripts 216 downloads