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 northeastern.edu>
citation("MSstatsLiP")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MSstatsLiP")
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("MSstatsLiP")| MSstatsLiP Proteolytic Workflow | HTML | R Script |
| MSstatsLiP Workflow: An example workflow and analysis of the MSstatsLiP package | HTML | R Script |
| Reference Manual |
Details
| biocViews | DifferentialExpression, ImmunoOncology, MassSpectrometry, Normalization, OneChannel, Proteomics, QualityControl, Software, TwoChannel |
| Version | 1.4.1 |
| In Bioconductor since | BioC 3.14 (R-4.1) (2.5 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 |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/Vitek-Lab/MSstatsLiP/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, covr, tinytest, gghighlight |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MSstatsLiP_1.4.1.tar.gz |
| Windows Binary | MSstatsLiP_1.4.1.zip |
| macOS Binary (x86_64) | MSstatsLiP_1.4.1.tgz |
| macOS Binary (arm64) | MSstatsLiP_1.4.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MSstatsLiP |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MSstatsLiP |
| Bioc Package Browser | https://code.bioconductor.org/browse/MSstatsLiP/ |
| Package Short Url | https://bioconductor.org/packages/MSstatsLiP/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.16 | Source Archive |