DOI: 10.18129/B9.bioc.MSstatsLiP  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see MSstatsLiP.

LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Bioconductor version: 3.16

Tools for LiP peptide and protein significance analysis. Provides functions for summarization, estimation of LiP peptide abundance, and detection of changes across conditions. Utilizes functionality across the MSstats family of packages.

Author: Devon Kohler [aut, cre], Tsung-Heng Tsai [aut], Ting Huang [aut], Mateusz Staniak [aut], Meena Choi [aut], Valentina Cappelletti [aut], Liliana Malinovska [aut], Olga Vitek [aut]

Maintainer: Devon Kohler <kohler.d at>

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


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HTML R Script MSstatsLiP Proteolytic Workflow
HTML R Script MSstatsLiP Workflow: An example workflow and analysis of the MSstatsLiP package
PDF   Reference Manual


biocViews DifferentialExpression, ImmunoOncology, MassSpectrometry, Normalization, OneChannel, Proteomics, QualityControl, Software, TwoChannel
Version 1.4.1
In Bioconductor since BioC 3.14 (R-4.1) (1.5 years)
License Artistic-2.0
Depends R (>= 4.1)
Imports dplyr, gridExtra, stringr, ggplot2, grDevices, MSstats, MSstatsConvert, data.table, Biostrings, MSstatsPTM, Rcpp, checkmate, factoextra, ggpubr, purrr, tibble, tidyr, tidyverse, scales, stats
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Suggests BiocStyle, knitr, rmarkdown, covr, tinytest, gghighlight
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