recipe bioconductor-timescape

Patient Clonal Timescapes

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-timescape/meta.yaml

TimeScape is an automated tool for navigating temporal clonal evolution data. The key attributes of this implementation involve the enumeration of clones, their evolutionary relationships and their shifting dynamics over time. TimeScape requires two inputs: (i) the clonal phylogeny and (ii) the clonal prevalences. Optionally, TimeScape accepts a data table of targeted mutations observed in each clone and their allele prevalences over time. The output is the TimeScape plot showing clonal prevalence vertically, time horizontally, and the plot height optionally encoding tumour volume during tumour-shrinking events. At each sampling time point (denoted by a faint white line), the height of each clone accurately reflects its proportionate prevalence. These prevalences form the anchors for bezier curves that visually represent the dynamic transitions between time points.

package bioconductor-timescape

(downloads) docker_bioconductor-timescape

Versions:
1.34.0-0,  1.30.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0, 

1.34.0-0,  1.30.0-0,  1.26.0-0,  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-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-timescape

to add into an existing workspace instead, run:

pixi add bioconductor-timescape

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-timescape

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-timescape

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-timescape:<tag>

(see bioconductor-timescape/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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