Dear Bioconductor developers, As the Bioconductor was released, I would like to present two new packages : DAPAR and Prostar.
DAPAR (Differential Analysis for Proteomics Analysis with R) is an R package for the analysis mass spectrometry-based discovery proteomics quantitative dataset. It is built on pre-existing Bioconductor packages devoted to proteomics and uses the MSnSet data structure from MSnbase. The package contains functions to import data from CSV files (such as those from Maxquant), and to export data to Excel files. DAPAR is made to guide the practitioner through the following classical steps of a protein-level data analysis: * *Descriptive statistics*: Exploration and visualization of your dataset with a detailed overview, which includes the following functionalities: Missing Values exploration, heatmap and correlation matrices, boxplots, expectation and variance distribution. * *Filtering*: DAPAR allows to filter proteins according to their number of missing values in each condition. * *Cross replicate normalisation*, with the following methods: (i) global rescaling (quantiles method, proportion method), (ii) median or mean centering (overall or within conditions), (iii) mean centering and scaling (overall or within conditions). * *Missing values imputation*, with the following methods: (i) for random occurences: k-nearest-neighbors, Bayesian Principal Component Analysis and Maximum Likelihood Estimation; for left censored missing values: Quantile Regression for Imputation of Left Censored data. * *Differential analysis*, according to a Welch t-test or a Limma moderated t-test. The package Prostar provides a GUI, based on Shiny, to interact with DAPAR. It offers a good flexibility to navigate through the different processing tools and plots available. The development of these two packages is very active and we work now on new functionalities and processing tools that will be available soon Do not hesitate to test this tool and to give me a feedback of your experience. Best Samuel Wieczorek -- Samuel Wieczorek Etude de la Dynamique des Proteomes (EDyP) http://edyp.fr/ Laboratoire Biologie a Grande Echelle (BGE) U1038 INSERM/CEA/UJF Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV) CEA/Grenoble 17 rue des Martyrs F-38054 Grenoble Cedex 9 Tel : 04 38 78 44 14 Tel : 04 38 78 34 40 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel