Added optional argument substitutions to addEditedAlleles"
Fixed condaEnv argument for addOnTargetScores
SNPs can now be annotated from a GRanges object.
Fixed splicing junction aa annotation when low scores
Fixed the accessor editedAlleles.
Added more annotation columns to the addEditedAlleles function.
Fixed getTssObjectFromTxObject for negative strand.
Added function addReinitiationFlag.
Added a warning message when having duplicated gRNAs.
Fixed intergenic annotation of alignments when non-standard chromosomes are found.
flattenGuideSet is now GuideSet2DataFrames.
Changed argument standard_chr_only to FALSE by default in the functions getSpacerAlignments and friends.
Updated the object guideSetExampleWithAlignments to contain the latest annotations.
Updated the object guideSetExampleFullAnnotation to contain the latest annotations.
Refactored addGeneAnnotation.
Added the function getPreMrnaSequence.
Added features for non-targeting controls (addNtcs).
New package crisprDesign, for the design of CRISPR gRNA.