rlist - A Toolbox for Non-Tabular Data Manipulation
Provides a set of functions for data manipulation with list objects, including mapping, filtering, grouping, sorting, updating, searching, and other useful functions. Most functions are designed to be pipeline friendly so that data processing with lists can be chained.
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9.80 score 112 dependents 3.1k scripts 41k downloads
NADIA - Missing Value-Aware Differential Abundance Analysis of DIA Proteomics Data
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.
Last updated
softwareproteomicsmassspectrometrydifferentialexpressionnormalizationqualitycontrolbatcheffect
6.12 score 51 scripts 31 downloads
