recipe bioconductor-siamcat

Statistical Inference of Associations between Microbial Communities And host phenoTypes

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/SIAMCAT.html

License:

GPL-3

Recipe:

/bioconductor-siamcat/meta.yaml

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:

2.6.0-0,  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, 

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 bioconductor-phyloseq:

>=1.46.0,<1.47.0

depends r-base:

>=4.3,<4.4.0a0

depends r-beanplot:

depends r-corrplot:

depends r-glmnet:

depends r-gridbase:

depends r-gridextra:

depends r-infotheo:

depends r-lgr:

depends r-liblinear:

depends r-lmertest:

depends r-matrixstats:

depends r-mlr3:

depends r-mlr3learners:

depends r-mlr3tuning:

depends r-paradox:

depends r-proc:

depends r-progress:

depends r-prroc:

depends r-rcolorbrewer:

depends r-scales:

depends r-stringr:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-siamcat

and update with::

   mamba update bioconductor-siamcat

To create a new environment, run:

mamba create --name myenvname bioconductor-siamcat

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-siamcat:<tag>

(see `bioconductor-siamcat/tags`_ for valid values for ``<tag>``)

Download stats

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