msImpute
This is thereleased version of msImpute; for the devel version, seemsImpute.
Imputation of label-free mass spectrometry peptides
Bioconductor version: Release (3.22)
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]
ORCID: 0000-0001-7513-6779
Maintainer: Soroor Hediyeh-zadeh <hediyehzadeh.s at wehi.edu.au>
citation("msImpute")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("msImpute")For older versions of R, please refer to the appropriateBioconductor 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 | ||
| NEWS | Text |
Details
| biocViews | MassSpectrometry,Proteomics,Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (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 |
| URL | |
| Bug Reports | https://github.com/DavisLaboratory/msImpute/issues |
See More
| Suggests | BiocStyle,knitr,rmarkdown,ComplexHeatmap,imputeLCMD |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | msImpute_1.20.0.tar.gz |
| Windows Binary (x86_64) | msImpute_1.20.0.zip |
| macOS Binary (x86_64) | msImpute_1.20.0.tgz |
| macOS Binary (arm64) | msImpute_1.20.0.tgz |
| 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 |