Alexey Sergushichev
Alexey Sergushichev
- [x] Microarray data from GEO with GEOquery package - [x] RNA-seq data from ARCHS4 - [ ] Data from recount2 project (https://jhubiostatistics.shinyapps.io/recount/ and corresponding R package). - [ ]...
- [x] Gene set enrichment with `fgsea`. - [ ] Phenotype prediction (with `phenopredict`?). - [x] Differential expression with limma and proper design matrix. - [x] Differential expression with DESeq2....
Calculating p-value and NES takes more time compared to the plot. If split the plot would be more responsive.
To add first K (2-3 in practice) annotations for rows and columns.
1. Open https://genome.ifmo.ru/phantasus/?geo=GSE27112 in Chrome 2. The window gets scrolled down so that you can't see the tab name. If opened in Firefox it seems to be OK, but a...
There should be an easy way to select the genes based on a pathway. Currently you have to get the gene list somewhere and put them in the search field....
Order of the columns should be mirrored at GSEA plot heatmap, so that if they are sorted on the front end, they are also sorted on backend
Add adjustment option to do limma::voom normalization for RNA-seq processing.