recipe bioconductor-cftools

Informatics Tools for Cell-Free DNA Study

Homepage:

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

License:

file LICENSE

Recipe:

/bioconductor-cftools/meta.yaml

The cfTools R package provides methods for cell-free DNA (cfDNA) methylation data analysis to facilitate cfDNA-based studies. Given the methylation sequencing data of a cfDNA sample, for each cancer marker or tissue marker, we deconvolve the tumor-derived or tissue-specific reads from all reads falling in the marker region. Our read-based deconvolution algorithm exploits the pervasiveness of DNA methylation for signal enhancement, therefore can sensitively identify a trace amount of tumor-specific or tissue-specific cfDNA in plasma. cfTools provides functions for (1) cancer detection: sensitively detect tumor-derived cfDNA and estimate the tumor-derived cfDNA fraction (tumor burden); (2) tissue deconvolution: infer the tissue type composition and the cfDNA fraction of multiple tissue types for a plasma cfDNA sample. These functions can serve as foundations for more advanced cfDNA-based studies, including cancer diagnosis and disease monitoring.

package bioconductor-cftools

versions:

1.2.0-0,  1.0.0-0

depends bioconductor-basilisk:

>=1.14.0,<1.15.0

depends bioconductor-basilisk:

>=1.14.1,<1.15.0a0

depends bioconductor-cftoolsdata:

>=1.0.0,<1.1.0

depends bioconductor-cftoolsdata:

>=1.0.0,<1.1.0a0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.1,<1.55.0a0

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:

depends r-r.utils:

depends r-rcpp:

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-cftools

and update with::

   mamba update bioconductor-cftools

To create a new environment, run:

mamba create --name myenvname bioconductor-cftools

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-cftools:<tag>

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

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