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

Imputation of label-free mass spectrometry peptides

Bioconductor version: Development (3.20)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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


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

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


biocViews MassSpectrometry, Proteomics, Software
Version 1.15.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 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
System Requirements python
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Suggests BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD
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Follow Installation instructions to use this package in your R session.

Source Package msImpute_1.15.0.tar.gz
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macOS Binary (x86_64) msImpute_1.15.0.tgz
macOS Binary (arm64) msImpute_1.15.0.tgz
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