Alexey Sergushichev

Hi, I'm running the example code `java -jar rdt-2.5.0-SNAPSHOT-jar-with-dependencies.jar -Q SMI -q "CC(O)CC(=O)OC(C)CC(O)=O.O[H]>>[H]OC(=O)CC(C)O.CC(O)CC(O)=O" -g -c -j AAM -f TEXT` and the result looks alright, but unexpectedly it returns non-zero exit...

Steps to reproduce: 1. Open any example dataset (say, gene expresion for Acute Myeloid Leukemia). 2. Open _File/Open_ menu. Go to preloaded tab. 3. Open any example dataset, again could...

Default amount for soft files

1

Is it possible to change the default amount for soft files to "data" for GPL files? The files would be smaller, because there will be no sample listing. In my...

1. Open a dataset with a row of zeroes. 2. Do a marker selection/signal to noise ratio. Some of the genes will have empty values (because of division by zero)....

Currently, if two points are close to each other, their labels will overlap. Instead, a kind of label layout algorithm should be used, similar to PCA plot.

Higher quality volcano plots

1

Currently, the points on volcano plots are rasterized with the dpi of the display. For publication quality they should be either in vector format or have higher dpi.

1. Open https://ctlab.itmo.ru/phantasus/ 2. Open file/URL/ http://ctlab.itmo.ru/~alserg/files/GSE53986.Ctrl.vs.LPS.gct Nothing happens, error in the console about mixed format. Open file/URL/ https://ctlab.itmo.ru/~alserg/files/GSE53986.Ctrl.vs.LPS.gct works fine

For log-scale it's useful to have a scale from minimum to maximum value on the scale