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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.
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:
install.packages("Prostar", lib="~/rlib")
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