Man pages for andreaskapou/processHTS
Process HTS Files and Data

annot_data	Annotation example data
bs_data	Bismark Cov formatted BS-Seq example data
create_enh_region	Create enhancer regions from gene annotation data.
create_methyl_region	Create methylation regions for each gene promoter.
create_prom_region	Create promoter regions from gene annotation data.
discard_bs_noise_reads	Discard BS-Seq noisy reads
discard_chr	Discard selected chromosomes
extract_fpkm	Extract FPKM from string
extract_gene_name	Extract gene name from string
hg19_data	Human Genome Assembly 19 chromosome sizes.
intersect_cgi_tss	Keep CGIs that intersect with promoter regions
minmax_scaling	Compute the min-max scaling
plot_prom_cpg_density	Plot promoter CpG density
plot_prom_cpg_hist	Plot promoter CpG histogram
pool_bs_seq_rep	Read and pool replicates from BS-Seq data
preprocess_bs_seq	Pre-process BS-Seq data in any given format
process_beatson_enh_wrap	Wrapper method for processing Beatson enhancer RNA-Seq and...
process_beatson_wrap	Wrapper method for processing Beatson RNA-Seq and BS-Seq HTS...
process_diff_beatson	Process differential BS-Seq and RNA-Seq Beatson HTS data
process_diff_haib_caltech	Process differential BS-Seq and RNA-Seq HAIB Caltech HTS data
process_haib_caltech_wrap	Wrapper method for processing ENCODE HAIB and Caltech HTS...
processHTS	'processHTS': A package for processing HTS data and files
read_annot_beatson	Read gene annotation file from Beatson
read_bs_bismark_cov	Read Bismark Cov formatted BS-Seq file
read_bs_encode_haib	Read ENCODE HAIB bed formatted BS-Seq file
read_chrom_size	Read genome chromosome sizes file.
read_encode_cgi	Read file containing CpG island locations
read_enh_beatson	Read Beatson bed formatted enhancer file
read_rna_beatson	Read Beatson bed formatted RNA-Seq file
read_rna_encode_caltech	Read ENCODE Caltech bed formatted RNA-Seq file
rnaseq_data	RNA-Seq example data
rrbs_data	RRBS example data