recipe bioconductor-islet

Individual-Specific ceLl typE referencing Tool

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-islet/meta.yaml

ISLET is a method to conduct signal deconvolution for general -omics data. It can estimate the individual-specific and cell-type-specific reference panels, when there are multiple samples observed from each subject. It takes the input of the observed mixture data (feature by sample matrix), and the cell type mixture proportions (sample by cell type matrix), and the sample-to-subject information. It can solve for the reference panel on the individual-basis and conduct test to identify cell-type-specific differential expression (csDE) genes. It also improves estimated cell type mixture proportions by integrating personalized reference panels.

package bioconductor-islet

versions:

1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-abind:

depends r-base:

>=4.3,<4.4.0a0

depends r-lme4:

depends r-matrix:

depends r-nnls:

depends r-purrr:

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-islet

and update with::

   mamba update bioconductor-islet

To create a new environment, run:

mamba create --name myenvname bioconductor-islet

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-islet:<tag>

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

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-islet/README.html)