Chicago pipeline for R studio?

[Dimitris Hat]

I am very new in bioinformatics and r language and was wondering if there is a very thorough pipeline, from start to finish for a CHi-C analysis. There is nothing in the pipelines tab.

[Mikhail Spivakov]

the short answer is no. however, you don't need to use R at all - all you need, once you've aligned the reads with HiCUP or equivalent Hi-C alignment software, is run bam2chicago.sh followed by Rscript runChicago.R - see the chicagoTools folder for these tools and their description.