recipe bioconductor-cfdnakit

Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-cfdnakit/meta.yaml

This package provides basic functions for analyzing shallow whole-genome sequencing (~0.3X or more) of cell-free DNA (cfDNA). The package basically extracts the length of cfDNA fragments and aids the vistualization of fragment-length information. The package also extract fragment-length information per non-overlapping fixed-sized bins and used it for calculating ctDNA estimation score (CES).

package bioconductor-cfdnakit

versions:

1.0.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-qdnaseq:

>=1.38.0,<1.39.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-ggplot2:

depends r-magrittr:

depends r-pscbs:

depends r-rlang:

requirements:

additional platforms:

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-cfdnakit

and update with::

   mamba update bioconductor-cfdnakit

To create a new environment, run:

mamba create --name myenvname bioconductor-cfdnakit

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-cfdnakit:<tag>

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

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