Index

B

block_for_run() (in module lib.chipseq)

C

cat() (in module lib.common) check_all_urls_found() (in module lib.common) check_url() (in module lib.common)

check_urls() (in module lib.common) ChIPSeqConfig (class in lib.patterns_targets) colData

D

dds deprecation_handler() (in module lib.common)

detect_peak_format() (in module lib.chipseq) download_and_postprocess() (in module lib.common)

F

fill_r1_r2() (in module lib.common)

filter_fastas() (in module lib.common)

G

get_references_dir() (in module lib.common) get_sampletable() (in module lib.common)

get_techreps() (in module lib.common) gff2gtf() (in module lib.common) gzipped() (in module lib.common)

I

is_paired_end() (in module lib.common)

L

lib.chipseq module

lib.common module load_config() (in module lib.common)

M

merged_input_for_ip() (in module lib.chipseq) module lib.chipseq lib.common

O

openfile() (in module lib.common)

P

peak_calling_dict() (in module lib.chipseq)

pluck() (in module lib.common)

R

references_dict() (in module lib.common) res_list

resolve_config() (in module lib.common) RNASeqConfig (class in lib.patterns_targets)

S

samples_for_run() (in module lib.chipseq)

SeqConfig (class in lib.patterns_targets)

T

twobit_to_fasta() (in module lib.common)

V

vsd