- recipe bioconductor-structtoolbox
Data processing & analysis tools for Metabolomics and other omics
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/structToolbox.html
- License:
GPL-3
- Recipe:
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.
- package bioconductor-structtoolbox¶
- Versions:
1.22.0-0,1.18.2-0,1.18.0-0,1.14.0-0,1.12.2-0,1.12.0-0,1.10.1-0,1.10.0-1,1.10.0-0,1.22.0-0,1.18.2-0,1.18.0-0,1.14.0-0,1.12.2-0,1.12.0-0,1.10.1-0,1.10.0-1,1.10.0-0,1.6.1-0,1.6.0-1,1.6.0-0,1.4.3-0,1.4.2-0,1.4.1-0,1.4.0-1,1.4.0-0,1.2.0-2,1.2.0-1,1.2.0-0,1.0.1-0,1.0.0-0- Depends:
on bioconductor-struct
>=1.22.0,<1.23.0on r-base
>=4.5,<4.6.0a0on r-ggplot2
on r-ggthemes
on r-gridextra
on r-scales
on r-sp
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install bioconductor-structtoolbox
to add into an existing workspace instead, run:
pixi add bioconductor-structtoolbox
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install bioconductor-structtoolbox
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-structtoolbox
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/bioconductor-structtoolbox:<tag>
(see bioconductor-structtoolbox/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-structtoolbox/README.html)
