recipe bioconductor-lace

Longitudinal Analysis of Cancer Evolution (LACE)

Homepage:

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

License:

file LICENSE

Recipe:

/bioconductor-lace/meta.yaml

LACE is an algorithmic framework that processes single-cell somatic mutation profiles from cancer samples collected at different time points and in distinct experimental settings, to produce longitudinal models of cancer evolution. The approach solves a Boolean Matrix Factorization problem with phylogenetic constraints, by maximizing a weighed likelihood function computed on multiple time points.

package bioconductor-lace

versions:

2.6.0-0,  2.4.0-0,  2.2.0-0,  1.6.0-0,  1.4.0-0,  1.2.1-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biomart:

>=2.58.0,<2.59.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-bsplus:

depends r-callr:

depends r-configr:

depends r-curl:

depends r-data.table:

depends r-data.tree:

depends r-doparallel:

depends r-dplyr:

depends r-dt:

depends r-forcats:

depends r-foreach:

depends r-fs:

depends r-ggplot2:

depends r-htmltools:

depends r-htmlwidgets:

depends r-igraph:

depends r-jsonlite:

depends r-logr:

depends r-matrix:

depends r-purrr:

depends r-rcolorbrewer:

depends r-readr:

depends r-rfast:

depends r-shiny:

depends r-shinybs:

depends r-shinydashboard:

depends r-shinyfiles:

depends r-shinyjs:

depends r-shinythemes:

depends r-shinyvalidate:

depends r-sortable:

depends r-stringi:

depends r-stringr:

depends r-svglite:

depends r-tidyr:

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-lace

and update with::

   mamba update bioconductor-lace

To create a new environment, run:

mamba create --name myenvname bioconductor-lace

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-lace:<tag>

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

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