Showing 10 of total 10 results (show query)
idslme
IDSL.FSA:Fragmentation Spectra Analysis (FSA)
The 'IDSL.FSA' package was designed to annotate standard .msp (mass spectra format) and .mgf (Mascot generic format) files using mass spectral entropy similarity, dot product (cosine) similarity, and normalized Euclidean mass error (NEME) followed by intelligent pre-filtering steps for rapid spectra searches. 'IDSL.FSA' also provides a number of modules to convert and manipulate .msp and .mgf files. The 'IDSL.FSA' workflow was integrated in the 'IDSL.CSA' and 'IDSL.NPA' packages introduced in <doi:10.1021/acs.analchem.3c00376>.
Maintained by Dinesh Barupal. Last updated 7 months ago.
fragmentation-spectramass-spectrometrymassbankmgfmgf-parsermspmsp-parserspectral-entropy
21.5 match 1 stars 3.48 score 2 dependentsbioc
MsBackendMgf:Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files
Mass spectrometry (MS) data backend supporting import and export of MS/MS spectra data from Mascot Generic Format (mgf) files. Objects defined in this package are supposed to be used with the Spectra Bioconductor package. This package thus adds mgf file support to the Spectra package.
Maintained by RforMassSpectrometry Package Maintainer. Last updated 2 months ago.
infrastructureproteomicsmassspectrometrymetabolomicsdataimport
8.5 match 5 stars 7.32 score 35 scripts 4 dependentsepiforesite
facilityepimath:Analyze Mathematical Models of Healthcare Facility Transmission
Calculate useful quantities for a user-defined differential equation model of infectious disease transmission among individuals in a healthcare facility. Input rates of transition between states of individuals with and without the disease-causing organism, distributions of states at facility admission, relative infectivity of transmissible states, and the facility length of stay distribution. Calculate the model equilibrium and the basic facility reproduction number, as described in Toth et al. (2025) <doi:10.1101/2025.02.21.25322698>.
Maintained by Damon Toth. Last updated 5 days ago.
9.3 match 5.18 scorebioc
MSnbase:Base Functions and Classes for Mass Spectrometry and Proteomics
MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.
Maintained by Laurent Gatto. Last updated 2 days ago.
immunooncologyinfrastructureproteomicsmassspectrometryqualitycontroldataimportbioconductorbioinformaticsmass-spectrometryproteomics-datavisualisationcpp
3.6 match 130 stars 12.81 score 772 scripts 36 dependentsyufree
enviGCMS:GC/LC-MS Data Analysis for Environmental Science
Gas/Liquid Chromatography-Mass Spectrometer(GC/LC-MS) Data Analysis for Environmental Science. This package covered topics such molecular isotope ratio, matrix effects and Short-Chain Chlorinated Paraffins analysis etc. in environmental analysis.
Maintained by Miao YU. Last updated 2 months ago.
environmentmass-spectrometrymetabolomics
3.4 match 17 stars 6.49 score 30 scripts 1 dependentsrobinhankin
hyper2:The Hyperdirichlet Distribution, Mark 2
A suite of routines for the hyperdirichlet distribution and reified Bradley-Terry; supersedes the 'hyperdirichlet' package; uses 'disordR' discipline <doi:10.48550/ARXIV.2210.03856>. To cite in publications please use Hankin 2017 <doi:10.32614/rj-2017-061>, and for Generalized Plackett-Luce likelihoods use Hankin 2024 <doi:10.18637/jss.v109.i08>.
Maintained by Robin K. S. Hankin. Last updated 3 days ago.
3.3 match 5 stars 6.01 score 38 scripts 1 dependentstaxonomicallyinformedannotation
tima:Taxonomically Informed Metabolite Annotation
This package provides the infrastructure to perform Taxonomically Informed Metabolite Annotation.
Maintained by Adriano Rutz. Last updated 6 days ago.
metabolite annotationchemotaxonomyscoring systemnatural productscomputational metabolomicstaxonomic distancespecialized metabolome
2.0 match 9 stars 6.55 score 32 scripts 2 dependentsbioc
MsBackendMassbank:Mass Spectrometry Data Backend for MassBank record Files
Mass spectrometry (MS) data backend supporting import and export of MS/MS library spectra from MassBank record files. Different backends are available that allow handling of data in plain MassBank text file format or allow also to interact directly with MassBank SQL databases. Objects from this package are supposed to be used with the Spectra Bioconductor package. This package thus adds MassBank support to the Spectra package.
Maintained by RforMassSpectrometry Package Maintainer. Last updated 18 days ago.
infrastructuremassspectrometrymetabolomicsdataimportmassbankspectra
1.8 match 3 stars 5.91 score 27 scripts