msImpute

DOI: 10.18129/B9.bioc.msImpute    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see msImpute.

Imputation of label-free mass spectrometry peptides

Bioconductor version: 3.12

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>

Installation

To install this package, start R (version "4.0") and enter:

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

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	1.0.0
In Bioconductor since	BioC 3.12 (R-4.0) (0.5 years)
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_1.0.0.tar.gz
Windows Binary	msImpute_1.0.0.zip
macOS 10.13 (High Sierra)	msImpute_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/msImpute
Source Repository (Developer Access)	git clone [email protected]:packages/msImpute
Package Short Url	https://bioconductor.org/packages/msImpute/
Package Downloads Report	Download Stats