Version: 1.44.1 Text: added support for bulge detection by integrating Cas-OFFinder. Version: 1.44.1 Text: tidied up most codes and modularized offTargetAnalysis(). Version: 1.44.1 Text: updated documentation and vignettes using Bioconductor style. Version: 1.44.1 Text: removed a few redundant/unnecessary parameters. Version: 1.44.1 Text: other minor bugs fixed. Version: 1.29.2 Text: added parameters such as predIndelFreq to allow the prediction of indels and their frequecies for Cas9 targeted sites Version: 1.29.1 Text: added parameter calculategRNAefficacyForOfftargets, default to TRUE. Version: 1.25.9 Text: added parameters allowing gRNA design for base editor system Version: 1.25.6 Text: added parameter ignore.strand to indidate whether gene annotation should be strand-specific Version: 1.25.5 Text: efficacy is calculated only for on-target Version: 1.25.4 Text: annotation is now strand-specific Version: 1.25.1 Category: NEW FEATURES Text: added paired.orientation parameteter Version: 1.9.12 Category: NEW FEATURES Text: added annotatePaired parameter Version: 1.9.12 Category: NEW FEATURES Text: added parallel processing Version: 1.9.6 Category: NEW FEATURES Text: added offTargetAnalysisOfPeakRegions function for GUIDE-seq analysis Version: 1.9.6 Category: offTargetAnalysisOfPeakRegions Text: Version: 1.9.3 Category: NEW FEATURES Text: support bed format inputFilePath for compare2Sequences Version: 1.9.3 Category: NEW FEATURES Text: added upstream and downstream parameters to compare2Sequences for bed input file Version: 1.9.3 Category: NEW FEATURES Text: added upstream.search and downstream.search in offTargetAnalysis for bed input file Version: 1.9.3 Category: NEW FEATURES Text: these features are particularly useful for annotating GUIDE-seq peaks Version: 1.9.2 Category: NEW FEATURES Text: summary file will contain all input gRNAs even there is no on target in the searching genome. This feature is useful to search for offtarget in a different genome Version: 1.9.2 Category: NEW FEATURES Text: support bed format inputFilePath for offTargetAnalysis Version: 1.9.1 Category: NEW FEATURES Text: added parameter allowed.mismatch.PAM to specify the number of degenerative bases in the PAM sequence. This feature is useful for specifying different PAM.pattern for offtarget search. Version: 1.7.6 Category: NEW FEATURES Text: added parameter foldgRNA to calculate the minimum free energy (mfe) of the secondary structure of the gRNA with gRNA backbone sequence. In addition, summary file also includes the difference of mfe between the secondary structure of gRNA backbone alone and the secondary structure of gRNA backbone with the variable region of the gRNA, and the bracket notation of the secondary structure of gRNA backbone with the variable region of the gRNA to facilitate gRNA selection. Version: 1.7.3 Category: NEW FEATURES Text: added parameter chromToExclude in offTargetAnalysis to specify chromosomes not to search for offtargets, which can be used to exclude haplotype blocks Version: 1.7.1 Category: BUG FIXES Text: only search for gRNAs for input sequences longer than gRNA.size plus PAM size Version: 1.5.6 Category: NEW FEATURES Text: added uniqueREsfor200total and uniqueREsfor100total in summary file to output RE sites that is unique in the 200 and 100 bp flanking gRNA region Version: 1.5.5 Category: NEW FEATURES Text: added useEfficacyFromInputSeq parameter in offTargetAnalysis function to allow user to select whether to use the gRNA efficacy calculated from the input sequence or the one from off-target analysis. This is useful when the input sequence is from a genome that is different from the off-target analysis genome Version: 1.5.4 Category: NEW FEATURES Text: rename the gRNAs containing Cas9 cut site instead of gRNA start end end. Also output the cut sites in genbank file Version: 1.5.3 Category: NEW FEATURES Text: gRNA efficacy is calcualted for compare2Sequence function and for offTargetAnalysis with chromToSearch="" Version: 1.5.2 Category: NEW FEATURES Text: filter gRNAs with one or both cut site overlap with RE pattern Version: 1.5.1 Category: NEW FEATURES Text: annotateOfftargets is separated from filterOfftarget function and is faster as well Version: 1.3.10 Category: NEW FEATURES Text: gRNAs are automatically output to a bed file for view in the UCSC genome browser Version: 1.3.8 Category: NEW FEATURES Text: Added calculategRNAefficiency to calculate gRNA cleavage efficiency using DoenchNBT2014 predictive logistic model Version: 1.3.7 Category: NEW FEATURES Text: Added searchDirection to compare2Sequences to allow search one against the other and many to many sequence search Version: 1.3.7 Category: NEW FEATURES Text: Added exception handling to catch no gRNA found error in compare2Sequences Version: 1.3.5 Category: BUG FIXES Text: TopN offtarget total score was sometimes missing for sequences containing gRNAs with less than 6 offtargets in version 1.3.3 Version: 1.3.3 Category: NEW FEATURES Text: Search for off-targets is much faster when more than 10 gRNAs are searched Version: 1.3.3 Category: NEW FEATURES Text: Added new optional parameter orgAnn in offTargetAnalysis Version: 1.3.3 Category: NEW FEATURES Text: Added gene ID and optional gene symbol in off-target output file Version: 1.3.3 Category: NEW FEATURES Text: Added gRNA target region, GC content of gRNA and number of Ts in the last 4 postion of gRNA (not including PAM sequence) in the summary output file