From my experience, there is few about CRISPR pooled screenings in R. One of them is ScreenBEAM. It uses a linear mixture model to determine significance at gene level by considering all the guides together at the same step in the analysis. However, it does not work very well for me.
There are other ways of analyze these screenings outside of R that are easy to use such the suggested MAGeCK or others such HiTSelect, BAGEL or CRISPR-Analyzer.
CRISPR-Analyzer is an online tool that could be useful and that recapitulates some of the mentioned methods in a single analysis. However, if you want to work from command line I would recommend you BAGEL for gene essentiality experiments and MAGeCK for other experimental setup (i.e, control vs treatment)
Sorry for not putting all the links but I can only put two at the moment!