R

The 7SK/P-TEFb snRNP controls ultraviolet radiation-induced transcriptional reprogramming

- The 7SK snRNA is dispensable for cell proliferation under standard growth conditions - After UV exposure, 7SK/P-TEFb is needed for proper stress response and cell survival - P-TEFb extracted from 7SK/P-TEFb triggers UV-induced general RNAPII pause release - P-TEFb from 7SK/P-TEFb supports activation of important UV-responsive genes

Chromatin and Transcription

Transcription by RNA polymerase II in the context of chromatin

BORDER proteins protect expression of neighboring genes by promoting 3' Pol II pausing in plants

Ensuring that one gene's transcription does not inappropriately affect the expression of its neighbors is a fundamental challenge to gene regulation in a genomic context. In plants, which lack homologs of animal insulator proteins, the mechanisms …

GeneNeighborhood: an R package to explore the direct neighbors of your favorite gene set

Visit [GeneNeighborhood on github](https://github.com/pgpmartin/GeneNeighborhood)

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.

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.

Core bioconductor packages for NGS data analysis