phantasus
phantasus copied to clipboard
ctlab
Visual exploratory analysis of gene expression data
When I try to import a volcano plot as an svg file into Adobe Illustrator it does not bring the actual dots for the genes. Everything else is fine (any...
I'm trying to combine multiple GSE datasets using the load dataset function > append columns, but I get the error "TypeError: newDataset.getRowMetadata is not a function." Is combining two different...
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)....
Having a shiny widget would be really useful since phantasus could be used with other features of shiny to make an app
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.
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
It used to be possible to save several datasets under one link. This was very useful, for example, for organizing public datasets relevant to the project. Old datasets that were...
@vlakam I was just thinking of a possibility to add DESeq2 normalization (median-based) in phantasus and displaying that as a heatmap. I was going through phantasus code to do that,...