DESeq2 in the browser
DESeq2 is a Bioconductor package for differential gene expression analysis.
Currently, DESeq2/Bioconductor aren't available in webR's binary repository. (webR allows you to run R code in the browser and comes with an R interpreter and default binary package repository.)
To run DESeq2 in the browser, I've compiled the package and its dependencies manually to the format required by webR. Live demo below.
The demo is a simple example of DESeq2 usage. You can paste your own count data, column data, and design formula and immediately see the results.
Demo: In-browser DESeq2
Count data (CSV, saved to /count_data.csv)
1
ensgene,SRR1039508,SRR1039509,SRR1039512,SRR1039513,SRR1039516,SRR1039517,SRR1039520,SRR10395212
ENSG00000000003,723.0,486.0,904.0,445.0,1170.0,1097.0,806.0,604.03
ENSG00000000005,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.04
ENSG00000000419,467.0,523.0,616.0,371.0,582.0,781.0,417.0,509.05
ENSG00000000457,347.0,258.0,364.0,237.0,318.0,447.0,330.0,324.06
ENSG00000000460,96.0,81.0,73.0,66.0,118.0,94.0,102.0,74.07
ENSG00000000938,0.0,0.0,1.0,0.0,2.0,0.0,0.0,0.08
ENSG00000000971,3413.0,3916.0,6e3,4308.0,6424.0,10723.0,5039.0,7803.09
ENSG00000001036,2328.0,1714.0,2640.0,1381.0,2165.0,2262.0,2175.0,1786.010
ENSG00000001084,670.0,372.0,692.0,448.0,917.0,807.0,744.0,685.011
ENSG00000001167,426.0,295.0,531.0,178.0,740.0,651.0,414.0,269.012
ENSG00000001460,191.0,182.0,287.0,137.0,256.0,234.0,173.0,189.013
ENSG00000001461,2232.0,1969.0,5252.0,2698.0,2699.0,2932.0,2495.0,3206.014
ENSG00000001497,556.0,513.0,619.0,355.0,666.0,770.0,517.0,440.015
ENSG00000001561,74.0,53.0,212.0,160.0,22.0,37.0,134.0,177.016
ENSG00000001617,560.0,372.0,934.0,436.0,706.0,725.0,581.0,641.017
ENSG00000001626,16.0,9.0,14.0,8.0,8.0,7.0,7.0,8.018
ENSG00000001629,1491.0,1204.0,2438.0,1041.0,2838.0,2727.0,1817.0,1747.019
ENSG00000001630,1014.0,807.0,1135.0,689.0,1374.0,1324.0,947.0,763.020
ENSG00000001631,694.0,725.0,1052.0,475.0,1137.0,1249.0,861.0,855.0Column data (CSV, saved to /col_data.csv)
2
SRR1039508,control,N61311,GSM12758623
SRR1039509,treated,N61311,GSM12758634
SRR1039512,control,N052611,GSM12758665
SRR1039513,treated,N052611,GSM12758676
SRR1039516,control,N080611,GSM12758707
SRR1039517,treated,N080611,GSM12758718
SRR1039520,control,N061011,GSM12758749
SRR1039521,treated,N061011,GSM1275875