recipe bioconductor-ancombc

Microbiome differential abudance and correlation analyses with bias correction

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-ancombc/meta.yaml

ANCOMBC is a package containing differential abundance (DA) and correlation analyses for microbiome data. Specifically, the package includes Analysis of Compositions of Microbiomes with Bias Correction 2 (ANCOM-BC2), Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC), and Analysis of Composition of Microbiomes (ANCOM) for DA analysis, and Sparse Estimation of Correlations among Microbiomes (SECOM) for correlation analysis. Microbiome data are typically subject to two sources of biases: unequal sampling fractions (sample-specific biases) and differential sequencing efficiencies (taxon-specific biases). Methodologies included in the ANCOMBC package are designed to correct these biases and construct statistically consistent estimators.

package bioconductor-ancombc

versions:

2.4.0-0,  2.2.0-0,  2.0.1-0,  1.4.0-0,  1.2.0-0,  1.0.5-0,  1.0.0-2

depends bioconductor-mia:

>=1.10.0,<1.11.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-treesummarizedexperiment:

>=2.10.0,<2.11.0

depends r-base:

>=4.3,<4.4.0a0

depends r-cvxr:

depends r-desctools:

depends r-doparallel:

depends r-dorng:

depends r-energy:

depends r-foreach:

depends r-gtools:

depends r-hmisc:

depends r-lme4:

depends r-lmertest:

depends r-mass:

depends r-matrix:

depends r-multcomp:

depends r-nloptr:

depends r-rdpack:

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-ancombc

and update with::

   mamba update bioconductor-ancombc

To create a new environment, run:

mamba create --name myenvname bioconductor-ancombc

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-ancombc:<tag>

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

Download stats

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