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 (3.19)

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 "4.4") 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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	MassSpectrometry, Proteomics, Software
Version	1.13.0
In Bioconductor since	BioC 3.12 (R-4.0) (3.5 years)
License	GPL (>=2)
Depends	R (> 4.1.0)
Imports	softImpute, methods, stats, graphics, pdist, reticulate, scran, data.table, FNN, matrixStats, limma, mvtnorm, tidyr, dplyr
System Requirements	python
URL
Bug Reports	https://github.com/DavisLaboratory/msImpute/issues

Suggests	BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
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
Package Short Url	https://bioconductor.org/packages/msImpute/
Package Downloads Report	Download Stats