Import data
import_bedGraph	Import bedGraph file
import_wiggle	Import wiggle data generated by the lab's ChIP-seq analysis pipeline
Data (functions returning data useful as input for downstream analyses)
get_chr_coordinates	Get chromosome coordinates
get_intergenic_regions	Get intergenic regions
get_Red1_summits	Get Red1 ChIP-seq summits in WT
get_dsb_hotspots	Get DSB hotspots
get_gff	Get GFF
Analyses
average_chr_signal	Average signal genome-wide and on each chromosome
signal_at_orf2	Signal at all ORFs genome-wide normalized to constant length (meta ORF)
signal_from_telomeres2	Collect signal from telomeres for all chromosome arms
signal_flanking_rDNA	Signal flanking rDNA
signal_mean_and_ci	Mean, SD, SEM, and confidence interval
opening_act2	Standard analysis of ChIP-seq experiments
opening_act2_batch_run	Batch run of opening_act2 function
compress_signal_track	Average signal variable over specified position windows
signal_track_correlation	Compute correlation between signal track data for two samples
binned_function	Apply function to bins of a numerical variable defined along a genome
facs_density_plot2	FACS density plot
spikein_normalization_factor	Compute spike-in normalization factor
Helpers
elapsed_time	Return elapsed time