Showing 2 of total 2 results (show query)
bioc
msPurity:Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
msPurity R package was developed to: 1) Assess the spectral quality of fragmentation spectra by evaluating the "precursor ion purity". 2) Process fragmentation spectra. 3) Perform spectral matching. What is precursor ion purity? -What we call "Precursor ion purity" is a measure of the contribution of a selected precursor peak in an isolation window used for fragmentation. The simple calculation involves dividing the intensity of the selected precursor peak by the total intensity of the isolation window. When assessing MS/MS spectra this calculation is done before and after the MS/MS scan of interest and the purity is interpolated at the recorded time of the MS/MS acquisition. Additionally, isotopic peaks can be removed, low abundance peaks are removed that are thought to have limited contribution to the resulting MS/MS spectra and the isolation efficiency of the mass spectrometer can be used to normalise the intensities used for the calculation.
Maintained by Thomas N. Lawson. Last updated 5 months ago.
massspectrometrymetabolomicssoftwarebioconductor-packagedimsfragmentationlc-mslc-msmsmass-spectrometryprecursor-ion-purity
15 stars 7.03 score 44 scriptsbioc
BulkSignalR:Infer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics
Inference of ligand-receptor (LR) interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics. BulkSignalR bases its inferences on the LRdb database included in our other package, SingleCellSignalR available from Bioconductor. It relies on a statistical model that is specific to bulk data sets. Different visualization and data summary functions are proposed to help navigating prediction results.
Maintained by Jean-Philippe Villemin. Last updated 3 months ago.
networkrnaseqsoftwareproteomicstranscriptomicsnetworkinferencespatial
5.22 score 15 scripts