NADIA
This is the development version of NADIA; to use it, please install the devel version of Bioconductor.
Missing Value-Aware Differential Abundance Analysis of DIA Proteomics Data
Bioconductor version: Development (3.24)
Provides an end-to-end workflow for differential abundance analysis of protein quantification data, with particular attention to missing values in data-independent acquisition (DIA) proteomics. Quantification reports exported from Spectronaut, DIA-NN and Proteome Discoverer for TMT and label-free experiments (DDA/DIA) are converted into a common data structure, normalised, optionally batch-corrected, imputed and analysed using limma or limpa. The package includes individual and two-stage imputation strategies that treat values assumed to be missing at random and missing not at random separately. Data-driven functions evaluate and rank normalisation and imputation workflows using simulated missingness or spike-in datasets with known ground truth, allowing method selection to be justified for each dataset. Results can be explored through interactive Highcharts visualisations, static ggplot2 and ComplexHeatmap figures, and sortable tables.
Author: Sergio Ciordia [aut, cre] 
Maintainer: Sergio Ciordia <sciordia at gmail.com>
citation("NADIA")):Sergio Ciordia. NADIA: Missing Value-Aware Differential Abundance Analysis of DIA Proteomics Data. doi:10.18129/B9.bioc.NADIA, R package version 0.99.3, https://bioconductor.org/packages/NADIA.
Generated from the package metadata; it may differ from the package's own citation.
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("NADIA")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("NADIA")| An introduction to NADIA | HTML |
| Batch correction: diagnose, correct, verify | HTML |
| Benchmarking with a spike-in: scoring against known truth | HTML |
| Choosing normalization and imputation methods | HTML |
| Input formats: reports and SummarizedExperiment objects | HTML |
| Missing values: what they mean and how to fill them | HTML |
| Pattern Profiler: identifying shared protein profiles | HTML |
| Results and export: sharing and preserving an analysis | HTML |
| Visualization: exploring and presenting results | HTML |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | BatchEffect, DifferentialExpression, MassSpectrometry, Normalization, Proteomics, QualityControl, Software |
| Version | 0.99.3 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL (>= 3) |
| Depends | R (>= 4.5.0) |
| Imports | dplyr, ggplot2, grDevices, grid, htmltools, htmlwidgets, jsonlite, limma, magrittr, methods, MsCoreUtils, pROC, RColorBrewer, rlang, rrcovNA, S4Vectors, stats, stringr, SummarizedExperiment, tibble, tidyr, tidyselect, tools, utils |
| System Requirements | |
| URL | https://github.com/sciordia/NADIA https://sciordia.github.io/NADIA/ |
| Bug Reports | https://github.com/sciordia/NADIA/issues |
See More
| Suggests | arrow, BERT, Biobase, BiocStyle, circlize, cluster, ComplexHeatmap, crosstalk, DBI, duckdb, e1071, ggsci, highcharter, impute, imputeLCMD, knitr, limpa, lme4, MASS, Mfuzz, mice, missForest, norm, paletteer, pcaMethods, reactable, rmarkdown, scales, testthat (>= 3.0.0), tidyHeatmap, vegan, viridis, vsn, withr |
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| Depends On Me | |
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| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/NADIA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/NADIA |
| Package Short Url | https://bioconductor.org/packages/NADIA/ |
| Package Downloads Report | Download Stats |