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)

ensgene,SRR1039508,SRR1039509,SRR1039512,SRR1039513,SRR1039516,SRR1039517,SRR1039520,SRR1039521
ENSG00000000003,723.0,486.0,904.0,445.0,1170.0,1097.0,806.0,604.0
ENSG00000000005,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
ENSG00000000419,467.0,523.0,616.0,371.0,582.0,781.0,417.0,509.0
ENSG00000000457,347.0,258.0,364.0,237.0,318.0,447.0,330.0,324.0
ENSG00000000460,96.0,81.0,73.0,66.0,118.0,94.0,102.0,74.0
ENSG00000000938,0.0,0.0,1.0,0.0,2.0,0.0,0.0,0.0
ENSG00000000971,3413.0,3916.0,6e3,4308.0,6424.0,10723.0,5039.0,7803.0
ENSG00000001036,2328.0,1714.0,2640.0,1381.0,2165.0,2262.0,2175.0,1786.0
ENSG00000001084,670.0,372.0,692.0,448.0,917.0,807.0,744.0,685.0
ENSG00000001167,426.0,295.0,531.0,178.0,740.0,651.0,414.0,269.0
ENSG00000001460,191.0,182.0,287.0,137.0,256.0,234.0,173.0,189.0
ENSG00000001461,2232.0,1969.0,5252.0,2698.0,2699.0,2932.0,2495.0,3206.0
ENSG00000001497,556.0,513.0,619.0,355.0,666.0,770.0,517.0,440.0
ENSG00000001561,74.0,53.0,212.0,160.0,22.0,37.0,134.0,177.0
ENSG00000001617,560.0,372.0,934.0,436.0,706.0,725.0,581.0,641.0
ENSG00000001626,16.0,9.0,14.0,8.0,8.0,7.0,7.0,8.0
ENSG00000001629,1491.0,1204.0,2438.0,1041.0,2838.0,2727.0,1817.0,1747.0
ENSG00000001630,1014.0,807.0,1135.0,689.0,1374.0,1324.0,947.0,763.0
ENSG00000001631,694.0,725.0,1052.0,475.0,1137.0,1249.0,861.0,855.0
1
ensgene,SRR1039508,SRR1039509,SRR1039512,SRR1039513,SRR1039516,SRR1039517,SRR1039520,SRR1039521
2
ENSG00000000003,723.0,486.0,904.0,445.0,1170.0,1097.0,806.0,604.0
3
ENSG00000000005,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
4
ENSG00000000419,467.0,523.0,616.0,371.0,582.0,781.0,417.0,509.0
5
ENSG00000000457,347.0,258.0,364.0,237.0,318.0,447.0,330.0,324.0
6
ENSG00000000460,96.0,81.0,73.0,66.0,118.0,94.0,102.0,74.0
7
ENSG00000000938,0.0,0.0,1.0,0.0,2.0,0.0,0.0,0.0
8
ENSG00000000971,3413.0,3916.0,6e3,4308.0,6424.0,10723.0,5039.0,7803.0
9
ENSG00000001036,2328.0,1714.0,2640.0,1381.0,2165.0,2262.0,2175.0,1786.0
10
ENSG00000001084,670.0,372.0,692.0,448.0,917.0,807.0,744.0,685.0
11
ENSG00000001167,426.0,295.0,531.0,178.0,740.0,651.0,414.0,269.0
12
ENSG00000001460,191.0,182.0,287.0,137.0,256.0,234.0,173.0,189.0
13
ENSG00000001461,2232.0,1969.0,5252.0,2698.0,2699.0,2932.0,2495.0,3206.0
14
ENSG00000001497,556.0,513.0,619.0,355.0,666.0,770.0,517.0,440.0
15
ENSG00000001561,74.0,53.0,212.0,160.0,22.0,37.0,134.0,177.0
16
ENSG00000001617,560.0,372.0,934.0,436.0,706.0,725.0,581.0,641.0
17
ENSG00000001626,16.0,9.0,14.0,8.0,8.0,7.0,7.0,8.0
18
ENSG00000001629,1491.0,1204.0,2438.0,1041.0,2838.0,2727.0,1817.0,1747.0
19
ENSG00000001630,1014.0,807.0,1135.0,689.0,1374.0,1324.0,947.0,763.0
20
ENSG00000001631,694.0,725.0,1052.0,475.0,1137.0,1249.0,861.0,855.0
21

Column data (CSV, saved to /col_data.csv)

id,dex,celltype,geo_id
SRR1039508,control,N61311,GSM1275862
SRR1039509,treated,N61311,GSM1275863
SRR1039512,control,N052611,GSM1275866
SRR1039513,treated,N052611,GSM1275867
SRR1039516,control,N080611,GSM1275870
SRR1039517,treated,N080611,GSM1275871
SRR1039520,control,N061011,GSM1275874
SRR1039521,treated,N061011,GSM1275875
1
id,dex,celltype,geo_id
2
SRR1039508,control,N61311,GSM1275862
3
SRR1039509,treated,N61311,GSM1275863
4
SRR1039512,control,N052611,GSM1275866
5
SRR1039513,treated,N052611,GSM1275867
6
SRR1039516,control,N080611,GSM1275870
7
SRR1039517,treated,N080611,GSM1275871
8
SRR1039520,control,N061011,GSM1275874
9
SRR1039521,treated,N061011,GSM1275875
10

Design formula

Output/Log

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DESeq2 in the browser

Demo: In-browser DESeq2

See also