recipe bioconductor-cicero

Predict cis-co-accessibility from single-cell chromatin accessibility data

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/cicero.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-cicero/meta.yaml

Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends monocle 2 for use in chromatin accessibility data.

package bioconductor-cicero

versions:

1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.1-0,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1, 

1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.1-0,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.0.14-0

depends bioconductor-biobase:

>=2.60.0,<2.61.0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-gviz:

>=1.44.0,<1.45.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-monocle:

>=2.28.0,<2.29.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends r-assertthat:

>=0.2.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

>=1.10.4

depends r-dplyr:

>=0.7.4

depends r-fnn:

>=1.1

depends r-ggplot2:

>=2.2.1

depends r-glasso:

>=1.8

depends r-igraph:

>=1.1.0

depends r-matrix:

>=1.2-12

depends r-plyr:

>=1.8.4

depends r-reshape2:

>=1.4.3

depends r-stringi:

depends r-stringr:

>=1.2.0

depends r-tibble:

>=1.4.2

depends r-tidyr:

depends r-vgam:

>=1.0-5

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-cicero

and update with::

   mamba update bioconductor-cicero

To create a new environment, run:

mamba create --name myenvname bioconductor-cicero

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-cicero:<tag>

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

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