Currently I use DESeq2 to analyse large scale CRIPSR loss-of-function screens (gene KO), where cell viability is measured with targeted sequencing, raw counts, for control and KO conditions.
All great so far although CRISPR has a couple of other artefacts that need to be taken in consideration. This is possible at the moment by applying a correction step after the fold-changes but I feel like a more integrated solution is possible. I think that DESeq/edgeR can be adapted to integrate a gene-wise correction method.
I know this is currently being addressed my multiple people but there isn't really an integrated approach yet. I would be very much interested to hear other's experience/opinions/suggestions about this.