Prostar

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Release: [![build release] (http://bioconductor.org/shields/build/release/bioc/Prostar.svg)] (https://bioconductor.org/checkResults/release/bioc-LATEST/Prostar/) Devel: [![build devel] (http://bioconductor.org/shields/build/devel/bioc/Prostar.svg)] (https://bioconductor.org/checkResults/devel/bioc-LATEST/Prostar/)

DAPAR and ProStaR are software tools to perform the statistical analysis of label-free XIC-based quantitative discovery proteomics experiments. DAPAR contains procedures to filter, normalize, impute missing value, aggregate peptide intensities, perform null hypothesis significance tests and select the most likely differentially abundant proteins with a corresponding false discovery rate. ProStaR is a graphical user interface that allows friendly access to the DAPAR functionalities through a web browser.

Installation

DAPAR and ProStaR are implemented in the R language and are available on the website of the Bioconductor project (http://www.bioconductor.org/). A complete tutorial and a toy dataset are accompanying the packages.

BiocManager::install("DAPAR2")

library(prostar)
prostar()

Install of the standalone version

cd ~; mkdir rlib mkdir rlib/www chmod -R 777 rlib/www

R CMD INSTALL Prostar_0.97.0.tar.gz –library=rlib If you would prefer to install the package from R, do this:

From CRAN

install.packages(“Prostar”, lib=”~/rlib”)

Usage

Example of a small size protein dataset.

Copy/paste to format your own dataset.

id    IntCond1    IntCond1    IntCond2    IntCond2
0    40679000    33460000    23513000    47514000
1    22472000    20529000    18878000    27066000
2    24181000    22307000    21765000    29650000
3    17831000    15288000    21161000    24255000
4    25557000    29942000    22358000    22992000
5    NA    NA    NA    NA
6    26948000    20690000    20022000    32127000
7    145130000    152030000    161860000    174660000
8    3750600    3680100    9091600    3803000
9    2288700000    2308300000    2457900000    2481200000
10    56216000    56733000    57767000    57121000
11    55116000    55531000    55141000    55985000
12    NA    NA    NA    10604000
13    NA    24846000    21564000    19663000
14    43910000    41853000    42121000    53375000
15    64318000    64018000    69304000    68975000
16    33044000    30683000    44981000    30866000
17    154570000    160330000    161860000    170290000
18    67461000    65409000    63535000    64638000

Contact

samuel.wieczorek@cea.fr, thomas.burger@cea.fr.