prolfqua
This is the development version of prolfqua; to use it, please install the devel version of Bioconductor.
Proteomics Label Free Quantification
Bioconductor version: Development (3.24)
The prolfqua package integrates essential steps of the mass spectrometry based label free quantification data analysis workflow: quality control, data normalization, protein aggregation, modeling, hypothesis testing and sample size estimation. We use prolfqua to : develop highly customizable, visually appealing, and interactive data analysis reports in pdf or HTML format; to visualize and model simple experimental designs with a single explanatory variable and complex experiments with multiple factors; to benchmark data acquisition, data preprocessing or data modeling methods. We developed and improved the package by applying the "Eating your own dog food" principle, when analysing dozens of proteomics datasets.
Author: Witold Wolski [aut]
, Functional Genomics Center Zurich [fnd], Christian Panse [cre]
Maintainer: Christian Panse <cp at fgcz.ethz.ch>
citation("prolfqua")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("prolfqua")
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("prolfqua")| Comparing Two Groups with prolfqua | HTML | R Script |
| Introduction to prolfqua | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | MassSpectrometry, Metabolomics, Normalization, Preprocessing, Proteomics, QualityControl, Software |
| Version | 0.99.4 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6) |
| Imports | circlize, ComplexHeatmap, dplyr, forcats, ggplot2, ggbeeswarm, ggrepel, limma, lme4, lmerTest, logistf, MASS, methods, plotly, progress, purrr, rlang, stringi, tidyselect, tidyr, tibble, UpSetR, withr |
| System Requirements | |
| URL | https://github.com/fgcz/prolfqua https://fgcz.github.io/prolfqua/ |
| Bug Reports | https://github.com/fgcz/prolfqua/issues |
See More
| Suggests | BiocCheck, BiocStyle, corrplot, covr, crosstalk, cyclocomp, devtools, goodpractice, gridExtra, KernSmooth, knitr, limpa, lintr, pkgdown, preprocessCore, rcmdcheck, Rfit, rmarkdown, roxygen2, S4Vectors, SummarizedExperiment, testthat, vsn |
| Linking To | |
| 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 | prolfqua_0.99.4.tar.gz |
| Windows Binary (x86_64) | prolfqua_0.99.3.zip |
| macOS Binary (big-sur-x86_64) | prolfqua_0.99.4.tgz |
| macOS Binary (sonoma-arm64) | prolfqua_0.99.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/prolfqua |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/prolfqua |
| Bioc Package Browser | https://code.bioconductor.org/browse/prolfqua/ |
| Package Short Url | https://bioconductor.org/packages/prolfqua/ |
| Package Downloads Report | Download Stats |