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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 (3.18)

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).

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 "4.3") and enter: 

if (!require("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")
msImpute: proteomics missing values imputation and diagnosis HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews MassSpectrometry, Proteomics, Software
Version 1.11.0
In Bioconductor since BioC 3.12 (R-4.0) (3 years)
License GPL (>=2)
Depends R (>= 3.5.0)
Imports softImpute, methods, stats, graphics, pdist, reticulate, scran, data.table, FNN, matrixStats, limma, mvtnorm, tidyr, dplyr
Linking To
Suggests BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD
System Requirements python
Enhances
URL
Bug Reports https://github.com/DavisLaboratory/msImpute/issues
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Depends On Me
Imports Me
Suggests Me
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Build Report  

Package Archives

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

Source Package msImpute_1.11.0.tar.gz
Windows Binary msImpute_1.11.0.zip
macOS Binary (x86_64) msImpute_1.11.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/msImpute
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/msImpute
Bioc Package Browser https://code.bioconductor.org/browse/msImpute/
Package Short Url https://bioconductor.org/packages/msImpute/
Package Downloads Report Download Stats