Package Recipe 'bioconductor-msimpute'

recipe bioconductor-msimpute

Imputation of label-free mass spectrometry peptides

Homepage:: https://bioconductor.org/packages/3.20/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:

1.20.0-0, 1.16.0-0, 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:

on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-scran >=1.38.0,<1.39.0
on r-base >=4.5,<4.6.0a0
on r-data.table
on r-dplyr
on r-fnn
on r-matrixstats
on r-mvtnorm
on r-pdist
on r-reticulate
on r-softimpute
on r-tidyr

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-msimpute

to add into an existing workspace instead, run:

pixi add bioconductor-msimpute

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-msimpute

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-msimpute

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-msimpute:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-msimpute/README.html)