msImpute

DOI: 10.18129/B9.bioc.msImpute    

This is the development version of msImpute; for the stable release version, see msImpute.

Imputation of label-free mass spectrometry peptides

Bioconductor version: Development (3.13)

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. Currently, msImpute completes missing values by low-rank approximation of the underlying data matrix.

Author: Soroor Hediyeh-zadeh [aut, cre]

Maintainer: Soroor Hediyeh-zadeh <hediyehzadeh.s at wehi.edu.au>

Citation (from within R, enter citation("msImpute")):

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("msImpute")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("msImpute")

 

HTML R Script msImpute: proteomics missing values imputation and diagnosis
PDF   Reference Manual
Text   NEWS

Details

biocViews MassSpectrometry, Proteomics, Software
Version 1.1.0
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
License GPL (>=2)
Depends R (>= 4.0)
Imports softImpute, methods, stats, graphics, pdist, reticulate, scran, data.table, FNN, matrixStats, rdetools, limma, mvtnorm
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD
SystemRequirements python
Enhances
URL
BugReports https://github.com/DavisLaboratory/msImpute/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package msImpute_1.1.0.tar.gz
Windows Binary msImpute_1.1.0.zip
macOS 10.13 (High Sierra) msImpute_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/msImpute
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/msImpute
Package Short Url https://bioconductor.org/packages/msImpute/
Package Downloads Report Download Stats

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