- recipe bioconductor-siamcat
Statistical Inference of Associations between Microbial Communities And host phenoTypes
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/SIAMCAT.html
- License:
GPL-3
- Recipe:
Pipeline for Statistical Inference of Associations between Microbial Communities And host phenoTypes (SIAMCAT). A primary goal of analyzing microbiome data is to determine changes in community composition that are associated with environmental factors. In particular, linking human microbiome composition to host phenotypes such as diseases has become an area of intense research. For this, robust statistical modeling and biomarker extraction toolkits are crucially needed. SIAMCAT provides a full pipeline supporting data preprocessing, statistical association testing, statistical modeling (LASSO logistic regression) including tools for evaluation and interpretation of these models (such as cross validation, parameter selection, ROC analysis and diagnostic model plots).
- package bioconductor-siamcat¶
- Versions:
2.14.0-0,2.10.0-0,2.6.0-0,2.4.0-0,2.2.0-0,1.14.0-0,1.12.0-0,1.10.0-1,1.10.0-0,2.14.0-0,2.10.0-0,2.6.0-0,2.4.0-0,2.2.0-0,1.14.0-0,1.12.0-0,1.10.0-1,1.10.0-0,1.8.0-0,1.6.0-0,1.4.0-1,1.2.0-0- Depends:
on bioconductor-phyloseq
>=1.54.0,<1.55.0on r-base
>=4.5,<4.6.0a0on r-beanplot
on r-corrplot
on r-glmnet
on r-gridbase
on r-gridextra
on r-infotheo
on r-lgr
on r-liblinear
on r-lmertest
on r-matrixstats
on r-mlr3
on r-mlr3learners
on r-mlr3tuning
on r-paradox
on r-proc
on r-progress
on r-prroc
on r-rcolorbrewer
on r-scales
on r-stringr
- 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-siamcat
to add into an existing workspace instead, run:
pixi add bioconductor-siamcat
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-siamcat
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-siamcat
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-siamcat:<tag>
(see bioconductor-siamcat/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-siamcat/README.html)
