recipe bioconductor-cellscape

Explores single cell copy number profiles in the context of a single cell tree

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/cellscape.html

License:

GPL-3

Recipe:

/bioconductor-cellscape/meta.yaml

CellScape facilitates interactive browsing of single cell clonal evolution datasets. The tool requires two main inputs: (i) the genomic content of each single cell in the form of either copy number segments or targeted mutation values, and (ii) a single cell phylogeny. Phylogenetic formats can vary from dendrogram-like phylogenies with leaf nodes to evolutionary model-derived phylogenies with observed or latent internal nodes. The CellScape phylogeny is flexibly input as a table of source-target edges to support arbitrary representations, where each node may or may not have associated genomic data. The output of CellScape is an interactive interface displaying a single cell phylogeny and a cell-by-locus genomic heatmap representing the mutation status in each cell for each locus.

package bioconductor-cellscape

(downloads) docker_bioconductor-cellscape

Versions:
1.34.0-0,  1.30.0-0,  1.24.0-0,  1.22.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0, 

1.34.0-0,  1.30.0-0,  1.24.0-0,  1.22.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0

Depends:

  • on r-base >=4.5,<4.6.0a0

  • on r-dplyr >=0.4.3

  • on r-gtools >=3.5.0

  • on r-htmlwidgets >=0.5

  • on r-jsonlite >=0.9.19

  • on r-reshape2 >=1.4.1

  • on r-stringr >=1.0.0

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-cellscape

to add into an existing workspace instead, run:

pixi add bioconductor-cellscape

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-cellscape

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-cellscape

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-cellscape:<tag>

(see bioconductor-cellscape/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.

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