Showing 5 of total 5 results (show query)
bioc
structToolbox:Data processing & analysis tools for Metabolomics and other omics
An extensive set of data (pre-)processing and analysis methods and tools for metabolomics and other omics, with a strong emphasis on statistics and machine learning. This toolbox allows the user to build extensive and standardised workflows for data analysis. The methods and tools have been implemented using class-based templates provided by the struct (Statistics in R Using Class-based Templates) package. The toolbox includes pre-processing methods (e.g. signal drift and batch correction, normalisation, missing value imputation and scaling), univariate (e.g. ttest, various forms of ANOVA, Kruskal–Wallis test and more) and multivariate statistical methods (e.g. PCA and PLS, including cross-validation and permutation testing) as well as machine learning methods (e.g. Support Vector Machines). The STATistics Ontology (STATO) has been integrated and implemented to provide standardised definitions for the different methods, inputs and outputs.
Maintained by Gavin Rhys Lloyd. Last updated 1 months ago.
workflowstepmetabolomicsbioconductor-packagedimslc-msmachine-learningmultivariate-analysisstatisticsunivariate
10 stars 6.26 score 12 scriptsbioc
struct:Statistics in R Using Class-based Templates
Defines and includes a set of class-based templates for developing and implementing data processing and analysis workflows, with a strong emphasis on statistics and machine learning. The templates can be used and where needed extended to 'wrap' tools and methods from other packages into a common standardised structure to allow for effective and fast integration. Model objects can be combined into sequences, and sequences nested in iterators using overloaded operators to simplify and improve readability of the code. Ontology lookup has been integrated and implemented to provide standardised definitions for methods, inputs and outputs wrapped using the class-based templates.
Maintained by Gavin Rhys Lloyd. Last updated 5 months ago.
5.91 score 76 scripts 3 dependentsbioc
MetMashR:Metabolite Mashing with R
A package to merge, filter sort, organise and otherwise mash together metabolite annotation tables. Metabolite annotations can be imported from multiple sources (software) and combined using workflow steps based on S4 class templates derived from the `struct` package. Other modular workflow steps such as filtering, merging, splitting, normalisation and rest-api queries are included.
Maintained by Gavin Rhys Lloyd. Last updated 5 months ago.
2 stars 5.75 score 5 scriptsbioc
OmicsMLRepoR:Search harmonized metadata created under the OmicsMLRepo project
This package provides functions to browse the harmonized metadata for large omics databases. This package also supports data navigation if the metadata incorporates ontology.
Maintained by Sehyun Oh. Last updated 10 days ago.
softwareinfrastructuredatarepresentationu24ca289073
5.40 score 14 scriptsbioc
metabolomicsWorkbenchR:Metabolomics Workbench in R
This package provides functions for interfacing with the Metabolomics Workbench RESTful API. Study, compound, protein and gene information can be searched for using the API. Methods to obtain study data in common Bioconductor formats such as SummarizedExperiment and MultiAssayExperiment are also included.
Maintained by Gavin Rhys Lloyd. Last updated 5 months ago.
4.60 score 8 scripts