Showing 12 of total 12 results (show query)
bioc
CompoundDb:Creating and Using (Chemical) Compound Annotation Databases
CompoundDb provides functionality to create and use (chemical) compound annotation databases from a variety of different sources such as LipidMaps, HMDB, ChEBI or MassBank. The database format allows to store in addition MS/MS spectra along with compound information. The package provides also a backend for Bioconductor's Spectra package and allows thus to match experimetal MS/MS spectra against MS/MS spectra in the database. Databases can be stored in SQLite format and are thus portable.
Maintained by Johannes Rainer. Last updated 3 months ago.
massspectrometrymetabolomicsannotationdatabasesmass-spectrometry
17 stars 8.35 score 69 scripts 1 dependentsbioc
fmcsR:Mismatch Tolerant Maximum Common Substructure Searching
The fmcsR package introduces an efficient maximum common substructure (MCS) algorithms combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules. The resulting flexible MCSs (FMCSs) are often larger than strict MCSs, resulting in the identification of more common features in their source structures, as well as a higher sensitivity in finding compounds with weak structural similarities. The fmcsR package provides several utilities to use the FMCS algorithm for pairwise compound comparisons, structure similarity searching and clustering.
Maintained by Thomas Girke. Last updated 5 months ago.
cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsmicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportclusteringproteomicsmetabolomicscpp
5 stars 7.03 score 60 scripts 1 dependentsbioc
MetaboAnnotation:Utilities for Annotation of Metabolomics Data
High level functions to assist in annotation of (metabolomics) data sets. These include functions to perform simple tentative annotations based on mass matching but also functions to consider m/z and retention times for annotation of LC-MS features given that respective reference values are available. In addition, the function provides high-level functions to simplify matching of LC-MS/MS spectra against spectral libraries and objects and functionality to represent and manage such matched data.
Maintained by Johannes Rainer. Last updated 4 months ago.
infrastructuremetabolomicsmassspectrometryannotationmass-spectromtry
15 stars 6.90 score 35 scriptsbioc
bioassayR:Cross-target analysis of small molecule bioactivity
bioassayR is a computational tool that enables simultaneous analysis of thousands of bioassay experiments performed over a diverse set of compounds and biological targets. Unique features include support for large-scale cross-target analyses of both public and custom bioassays, generation of high throughput screening fingerprints (HTSFPs), and an optional preloaded database that provides access to a substantial portion of publicly available bioactivity data.
Maintained by Thomas Girke. Last updated 5 months ago.
immunooncologymicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportbioinformaticsproteomicsmetabolomics
5 stars 6.70 score 46 scriptsbioc
RMassBank:Workflow to process tandem MS files and build MassBank records
Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.
Maintained by RMassBank at Eawag. Last updated 5 months ago.
immunooncologybioinformaticsmassspectrometrymetabolomicssoftwareopenjdk
6.02 score 26 scriptsbioc
MetID:Network-based prioritization of putative metabolite IDs
This package uses an innovative network-based approach that will enhance our ability to determine the identities of significant ions detected by LC-MS.
Maintained by Zhenzhi Li. Last updated 5 months ago.
assaydomainbiologicalquestioninfrastructureresearchfieldstatisticalmethodtechnologyworkflowstepnetworkkegg
1 stars 5.74 score 110 scriptsbioc
eiR:Accelerated similarity searching of small molecules
The eiR package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach.
Maintained by Thomas Girke. Last updated 2 months ago.
cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsmicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportclusteringproteomicsmetabolomics
3 stars 5.51 score 12 scriptsbioc
customCMPdb:Customize and Query Compound Annotation Database
This package serves as a query interface for important community collections of small molecules, while also allowing users to include custom compound collections.
Maintained by Yuzhu Duan. Last updated 5 months ago.
softwarecheminformaticsannotationhubsoftware
2 stars 4.78 score 4 scripts
hpetren
chemodiv:Analysing Chemodiversity of Phytochemical Data
Quantify and visualise various measures of chemical diversity and dissimilarity, for phytochemical compounds and other sets of chemical composition data. Importantly, these measures can incorporate biosynthetic and/or structural properties of the chemical compounds, resulting in a more comprehensive quantification of diversity and dissimilarity. For details, see Petrén, Köllner and Junker (2023) <doi:10.1111/nph.18685>.
Maintained by Hampus Petrén. Last updated 2 years ago.
5 stars 4.57 score 15 scripts
cct-datascience
volcalc:Calculate Volatility of Chemical Compounds
Calculate estimated relative volatility index values for organic compounds based on functional group contributions. Calculation uses the SIMPOL.1 method in Prankow and Asher (2008) <doi:10.5194/acp-8-2773-2008> or modified SIMPOL.1 method as in Meredith et al. (2023) <doi:10.5194/acp-8-2773-2008>.
Maintained by Kristina Riemer. Last updated 6 months ago.
cheminformaticschemometricsmetabolomics
5 stars 4.30 score 7 scripts
hanjunwei-lab
DrugSim2DR:Predict Drug Functional Similarity to Drug Repurposing
A systematic biology tool was developed to repurpose drugs via a drug-drug functional similarity network. 'DrugSim2DR' first predict drug-drug functional similarity in the context of specific disease, and then using the similarity constructed a weighted drug similarity network. Finally, it used a network propagation algorithm on the network to identify drugs with significant target abnormalities as candidate drugs.
Maintained by Junwei Han. Last updated 2 years ago.
2 stars 4.00 score 2 scripts