recipe bioconductor-zitools

Analysis of zero-inflated count data

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/zitools.html

License:

BSD_3_clause + file LICENSE

Recipe:

/bioconductor-zitools/meta.yaml

zitools allows for zero inflated count data analysis by either using down-weighting of excess zeros or by replacing an appropriate proportion of excess zeros with NA. Through overloading frequently used statistical functions (such as mean, median, standard deviation), plotting functions (such as boxplots or heatmap) or differential abundance tests, it allows a wide range of downstream analyses for zero-inflated data in a less biased manner. This becomes applicable in the context of microbiome analyses, where the data is often overdispersed and zero-inflated, therefore making data analysis extremly challenging.

package bioconductor-zitools

versions:

1.0.0-0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-deseq2:

>=1.46.0,<1.47.0

depends bioconductor-matrixgenerics:

>=1.18.0,<1.19.0

depends bioconductor-phyloseq:

>=1.50.0,<1.51.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-dplyr:

depends r-ggplot2:

depends r-magrittr:

depends r-matrixstats:

depends r-pscl:

depends r-rcolorbrewer:

depends r-reshape2:

depends r-tibble:

depends r-tidyr:

depends r-vgam:

requirements:

additional platforms:

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-zitools

and update with::

   mamba update bioconductor-zitools

To create a new environment, run:

mamba create --name myenvname bioconductor-zitools

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-zitools:<tag>

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

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