The most recent version of ATACseqQC at http://bioconductor.org/packages/devel/bioc/html/ATACseqQC.html should run faster.
... Hi, could you please try with upstream.cutoff = 0, downstream.cutoff = 0? Also could you please provide your R session information by typing sessionInfo()? Thanks!
GUIDEseq package can be used to analyze CIRCLE-seq too. During the preprocessing steps, you will not need to remove adaptors introduced in the GUIDE-seq protocol. In addition, you will need to set the max.R1.len =150 and max.R2.len = 150 using the GUIDEseqAnalysis function in GUIDEseq packag ...
Here is a description of the parameter useEfficacyFromInputSeq.
Default FALSE. If set to TRUE, summary file will contain gRNA efficacy calculated from input sequences instead of from off-target analysis. Set it to TRUE if the input sequence is from a different species than the one used for o ...
Thanks for taking time to post the question! https://bioconductor.org/packages/3.5/BiocViews.html#___BSgenome lists BSgenomes that can be directly used as input to CRISPRseek .
For detailed information on how to use the package, please read the user guide at http://bioconductor.org/package ...
Thanks for the great question!
Different applications place different emphasis on efficacy vs offTarget score. For example, in vitro screening assays are more interested in efficacy score, while therapeutic studies cannot tolerate even small offTarget effects. Therefore, it is very hard to c ...