I have been recently involved in a project trying to find the relationship between histone modifications (ChIP-Seq) and gene expression (RNA-Seq). Tried different machine learning algorithms.
I wanted to test correlations between biological replicates of several samples in a ChIP-Seq experiment. Output better to be data frame with different features and samples.
Palm and Psion (EPOC) are still my favourite tools today, although they are quite different: Palm is purely single-tasking, while Psion is real multi-tasking. Although they are both around 20 years old, there are still resources on the web.
The Psion 5MX has a comfortable keyboard, a clear screen, a pocket size, a good system, but incapbability to communicate with moden devices.
I was excited to buy one out-of-stock RPi 4 but unfortunatelly I couln't boost it with normal phone charger.
I am trying to plot enriched functional clusters on each chromosome, like ideograms.
This is originally from the work that I was trying to find enriched functional clusters on chromosomes. I made 5-gene sliding 50-gene blocks and tested functional enrichment in each block.
The R package topGO can perform GO enrichment using Fisher's Exact test, which is based on gene counts, as well as Kolmogorov-Smirnov like test, which is based on gene scores.