recipe bioconductor-pirat

Precursor or Peptide Imputation under Random Truncation

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-pirat/meta.yaml

Pirat enables the imputation of missing values (either MNARs or MCARs) in bottom-up LC-MS/MS proteomics data using a penalized maximum likelihood strategy. It does not require any parameter tuning, it models the instrument censorship from the data available. It accounts for sibling peptides correlations and it can leverage complementary transcriptomics measurements.

package bioconductor-pirat

versions:

1.0.0-0

depends bioconductor-basilisk:

>=1.18.0,<1.19.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-ggplot2:

depends r-invgamma:

depends r-mass:

depends r-progress:

depends r-reticulate:

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-pirat

and update with::

   mamba update bioconductor-pirat

To create a new environment, run:

mamba create --name myenvname bioconductor-pirat

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-pirat:<tag>

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

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Link to this page

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