recipe bioconductor-zfpkm

A suite of functions to facilitate zFPKM transformations

Homepage:

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

License:

GPL-3 | file LICENSE

Recipe:

/bioconductor-zfpkm/meta.yaml

Perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113). Reference recommends using zFPKM > -3 to select expressed genes. Validated with encode open/closed chromosome data. Works well for gene level data using FPKM or TPM. Does not appear to calibrate well for transcript level data.

package bioconductor-zfpkm

(downloads) docker_bioconductor-zfpkm

versions:
1.24.0-0,  1.22.0-0,  1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0, 

1.24.0-0,  1.22.0-0,  1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-checkmate:

depends r-dplyr:

depends r-ggplot2:

depends r-tidyr:

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-zfpkm

and update with::

   mamba update bioconductor-zfpkm

To create a new environment, run:

mamba create --name myenvname bioconductor-zfpkm

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-zfpkm:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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