All functions
chr_coverage_plot	Average chromosome signal (coverage) dot plot
chr_coverage	Average signal per chromosome
facs_density_plot	FACS density plot
FE2	Microarray probe log2 ratios
genome_average	Calculate genome-wide average signal
gff_get_attribute	Parse gff field
gff_read	Read gff file
	hwglabr: A compilation of functions used frequently by Hochwagen lab members.
opening_act_batch_run	Batch run of opening_act function
opening_act	Standard analysis of ChIP-seq experiments
order_chromosomes	Order chromosome column by chromosome length
plot_gene_arrow	Plot genes on an R wiggle plot
readall_tab	Load wiggle data
remove_centromeres	Remove centromeric regions from wiggle data
rna_seq_analysis	Wrapper function to run edgeR analysis of summarized reads from RNA-seq experiment
signal_at_conv_average_plot	Line plot of average signal between convergent genes
signal_at_conv	Signal between all convergent genes genome-wide
signal_at_intergen_average_plot	Line plot of average signal on intergenic regions
signal_at_intergen	Signal at intergenic regions between convergent, divergent or tandem genes genome-wide
signal_at_orf_average_plot	Line plot of average signal on ORFs
signal_at_orf_se	Signal around ORF start or end positions
signal_at_orf	Signal at all ORFs genome-wide (meta ORF)
signal_at_rDNA	Signal flanking rDNA
signal_at_summit	Signal around all bedfile midpoints
signal_average	Calculate average signal by position
signal_from_telomeres_average	Compute mean signal and SD by position of output of signal_from_telomeres
signal_from_telomeres	Collect signal from telomeres for all chromosome arms
signal_per_orf_length	Mean signal for all ORFs genome-wide
wiggle_compress	Compress wiggle data
wiggle_correlation	Correlation between two ChIP-seq experiments
wiggle_plot	Wiggle data line plot
wiggle_scatter_plot	To make a scatter plot comparison of two wiggle files
wiggle_scatter	To make a scatter plot comparison of two wiggle files
wiggle_signal_average	Calculate genome-wide signal average in wiggle data
wiggle_smooth	Sliding window smooth of wiggle data