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flowml

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A Backend for a 'nextflow' Pipeline that Performs Machine-Learning-Based Modeling of Biomedical Data

View on CRAN: Click here

Download and install flowml package within the R console
Install from CRAN:

 install.packages("flowml")

Install from Github:

 library("remotes")

                        install_github("cran/flowml")

Install by package version:

 library("remotes")

                        install_version("flowml", "0.1.3")

Attach the package and use:

 library("flowml")

Maintained by
Sebastian Malkusch
[Scholar Profile | Author Map]

All associated links for this package

First Published: 2023-10-09

Latest Update: 2024-02-16

Description:

Provides functionality to perform machine-learning-based modeling in a computation pipeline. Its functions contain the basic steps of machine-learning-based knowledge discovery workflows, including model training and optimization, model evaluation, and model testing. To perform these tasks, the package builds heavily on existing machine-learning packages, such as 'caret' and associated packages. The package can train multiple models, optimize model hyperparameters by performing a grid search or a random search, and evaluates model performance by different metrics. Models can be validated either on a test data set, or in case of a small sample size by k-fold cross validation or repeated bootstrapping. It also allows for 0-Hypotheses generation by performing permutation experiments. Additionally, it offers methods of model interpretation and item categorization to identify the most informative features from a high dimensional data space. The functions of this package can easily be integrated into computation pipelines (e.g. 'nextflow' ) and hereby improve scalability, standardization, and re-producibility in the context of machine-learning.

How to cite:

Sebastian Malkusch (2023). flowml: A Backend for a 'nextflow' Pipeline that Performs Machine-Learning-Based Modeling of Biomedical Data. R package version 0.1.3, https://cran.r-project.org/web/packages/flowml. Accessed 18 Sep. 2026.

Previous versions and publish date:

(2026-07-09 07:39), 0.1.2 (2023-10-09 14:50), 0.1.3 (2024-02-16 11:40)

Other packages that cited flowml R package

View flowml citation profile

Other R packages that flowml depends, imports, suggests or enhances

View flowml dependency map

Complete documentation for flowml

View documentation PDF

Functions, R codes and Examples using the flowml R package

Some associated functions: Resampler . create_parser . create_resample_experiment . fml_bootstrap . fml_example . fml_interpret . fml_train . fml_validate . format_y . run_abc_analysis .
Some associated R codes: fml_bootstrap.R . fml_categorize.R . fml_example.R . fml_format_response.R . fml_globals.R . fml_grids.R . fml_interpret.R . fml_parser.R . fml_resample.R . fml_resampler.R . fml_train.R . fml_validate.R . Full flowml package functions and examples

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