Package index • breakinspectoR

All functions

breakinspectoR(): breakinspectoR

get_guide_and_pam(): get_guide_and_pam

manhattan_plot(): manhattan_plot Manhattan plot showing on/off-targets detected organized by chromosomal position with bar height representing read count (number of breaks).

msg(): msg

breakinspectoR_examples: Offtargets detected within the BreakTag test data included in this package

breakinspectoR_examples: Scission profile of the offtargets detected within the BreakTag test data included in this package

plot_blunt_rate_density(): plot_blunt_rate_density Density Plot for Blunt Rate Distribution.

plot_genomic_position(): plot_genomic_position Plot the genomic position of the breaks, identifying detected on-/off-targets.

plot_guide_fidelity(): plot_guide_fidelity

plot_mismatch_freq(): plot_mismatch_freq Plot the frequency of mismatches per offtarget.

plot_offtargets_by_pam(): plot_offtargets_by_pam Plot the count of offtargets by the different PAMs

plot_overhang_size(): plot_overhang_size Plots the proportion of blunt and staggered reads by size.

plot_pam_composition(): plot_pam_composition Plots the proportion nucleotide usage per position of the PAM.

plot_pam_logo(): plot_pam_logo PAM prefence Analysis.

plot_position_cutsite(): plot_position_cutsite Plot the frequency of the position of the cutsite relative to the guide.

plot_relative_activity(): plot_relative_activity Plot Cas9 activity of a list of multiple gRNA offtargets relative to one experiment.

plot_scission_profile(): plot_scission_profile Plot ratios of blunt vs. staggered signal for each OT detected.

plot_sequence_composition(): plot_sequence_composition Sequence composition of off-target sites.

plot_specificity(): plot_specificity Plot Cas9 specificity of a list of multiple gRNA offtargets.

read_targets(): read_targets

reduceOT(): reduceOT

scission_profile_analysis(): scission_profile_analysis

shiny_BTmotif(): shiny_BTmotif Launch an interactive web interface.

shiny_bluntPred(): shiny_bluntPred Launch an interactive web interface.

test_offtargets(): test_offtargets