[Bioc-devel] New packages: DAPAR and Prostar

[Samuel Wieczorek]

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


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