recipe bioconductor-msimpute

Imputation of label-free mass spectrometry peptides

Homepage:

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

License:

GPL (>=2)

Recipe:

/bioconductor-msimpute/meta.yaml

MsImpute is a package for imputation of peptide intensity in proteomics experiments. It additionally contains tools for MAR/MNAR diagnosis and assessment of distortions to the probability distribution of the data post imputation. The missing values are imputed by low-rank approximation of the underlying data matrix if they are MAR (method = "v2"), by Barycenter approach if missingness is MNAR ("v2-mnar"), or by Peptide Identity Propagation (PIP).

package bioconductor-msimpute

versions:

1.12.0-0,  1.10.0-0,  1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1,  1.0.0-0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-scran:

>=1.30.0,<1.31.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-dplyr:

depends r-fnn:

depends r-matrixstats:

depends r-mvtnorm:

depends r-pdist:

depends r-reticulate:

depends r-softimpute:

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-msimpute

and update with::

   mamba update bioconductor-msimpute

To create a new environment, run:

mamba create --name myenvname bioconductor-msimpute

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-msimpute:<tag>

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

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