Package Recipe 'bioconductor-lace'

recipe bioconductor-lace

Longitudinal Analysis of Cancer Evolution (LACE)

Homepage:: https://bioconductor.org/packages/3.20/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:

2.14.0-0, 2.10.0-0, 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,

2.14.0-0, 2.10.0-0, 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:

on bioconductor-biomart >=2.66.0,<2.67.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-bsplus
on r-callr
on r-configr
on r-curl
on r-data.table
on r-data.tree
on r-doparallel
on r-dplyr
on r-dt
on r-forcats
on r-foreach
on r-fs
on r-ggplot2
on r-htmltools
on r-htmlwidgets
on r-igraph
on r-jsonlite
on r-logr
on r-matrix
on r-purrr
on r-rcolorbrewer
on r-readr
on r-rfast
on r-shiny
on r-shinybs
on r-shinydashboard
on r-shinyfiles
on r-shinyjs
on r-shinythemes
on r-shinyvalidate
on r-sortable
on r-stringi
on r-stringr
on r-svglite
on r-tidyr

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-lace

to add into an existing workspace instead, run:

pixi add bioconductor-lace

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-lace

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-lace

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-lace:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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-lace/README.html)