recipe bioconductor-sccomp

Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-sccomp/meta.yaml

A robust and outlier-aware method for testing differential tissue composition from single-cell data. This model can infer changes in tissue composition and heterogeneity, and can produce realistic data simulations based on any existing dataset. This model can also transfer knowledge from a large set of integrated datasets to increase accuracy further.

package bioconductor-sccomp

versions:

1.4.0-0,  1.1.0-1,  1.1.0-0

depends bioconductor-singlecellexperiment:

>=1.22.0,<1.23.0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-bh:

>=1.66.0

depends r-boot:

depends r-dplyr:

depends r-forcats:

depends r-ggplot2:

depends r-ggrepel:

depends r-glue:

depends r-lifecycle:

depends r-magrittr:

depends r-patchwork:

depends r-purrr:

depends r-rcpp:

>=0.12.0

depends r-rcppeigen:

>=0.3.3.3.0

depends r-rcppparallel:

>=5.0.1

depends r-readr:

depends r-rlang:

depends r-rstan:

>=2.18.1

depends r-rstantools:

>=2.1.1

depends r-scales:

depends r-seuratobject:

depends r-stanheaders:

>=2.18.0

depends r-stringr:

depends r-tibble:

depends r-tidyr:

depends r-tidyselect:

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-sccomp

and update with::

   mamba update bioconductor-sccomp

To create a new environment, run:

mamba create --name myenvname bioconductor-sccomp

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-sccomp:<tag>

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

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Link to this page

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