R

Generate random genes as GRanges

Generating random genome annotations For different purposes, I often need to create random gene/features annotations. I usually need these annotations as a GRanges object (see the GenomicRanges package). I searched a bit on the internet but couldn’t really find what I was looking for. I want to be able to control the following parameters: Number of genes Gene sizes (~gaussian distribution with upper and lower bounds as parameters)

Nicer scatter plots in GGgally ggpairs-ggduo

GGally is an extension of ggplot2. I use it mainly as a replacement/refinement of pairs in base R. Here, I want to replace the default scatter plot used to compare 2 continuous variables with something nicer, especially adapted to plotting large number of points. Load the library and some RNA-seq data: library(GGally) library(airway) data(airway) The airway dataset contains data for 4 cell lines treated or not with dexamethasone:

Chromatin and Transcription

Transcription by RNA polymerase II in the context of chromatin