Index

Symbols | B | C | D | E | G | I | M | O | P | S | V | W

Symbols

[basics], [1], [2]
[contamination]
[species], [1], [2]

B

bwa() (chilin2.modules.bwa.dc method)

C

chilin2 (module)
chilin2.modules (module)
chilin2.modules.bwa (module)
chilin2.modules.bwa.dc (module)
chilin2.modules.bwa.qc (module)
chilin2.modules.ceas (module)
chilin2.modules.ceas.dc (module)
chilin2.modules.ceas.qc (module)
chilin2.modules.config (module)
chilin2.modules.config.config (module)
chilin2.modules.config.helpers (module)
chilin2.modules.conservation (module)
chilin2.modules.conservation.dc (module)
chilin2.modules.conservation.qc (module)
chilin2.modules.contamination (module)
chilin2.modules.contamination.dc (module)
chilin2.modules.contamination.qc (module)
chilin2.modules.contamination.tex (module)
chilin2.modules.enrichment (module)
chilin2.modules.enrichment.dc (module)
chilin2.modules.fastqc.dc (module)
chilin2.modules.fastqc.qc (module)
chilin2.modules.fastqc.tex (module)
chilin2.modules.frip (module)
chilin2.modules.frip.dc (module)
chilin2.modules.frip.qc (module)
chilin2.modules.library (module)
chilin2.modules.library.dc (module)
chilin2.modules.library.qc (module)
chilin2.modules.macs (module)
chilin2.modules.macs.dc (module)
chilin2.modules.macs2_fragment (module)
chilin2.modules.macs2_fragment.dc (module)
chilin2.modules.macs2_fragment.qc (module)
chilin2.modules.mdseqpos (module)
chilin2.modules.mdseqpos.dc (module)
chilin2.modules.mdseqpos.qc (module)
chilin2.modules.mdseqpos.tex (module)
chilin2.modules.regulatory (module)
chilin2.modules.regulatory.dc (module)
chilin2.modules.replicates (module)
chilin2.modules.replicates.dc (module)
chilin2.modules.replicates.qc (module)
chilin2.modules.summary (module)
chilin2.modules.summary.qc_json_summary (module)
chilin2.modules.summary.qc_summary_table (module)
chrom_len
conservation

D

dhs

E

environment variable
[basics], [1], [2], [3]
[conservation]
[contamination], [1]
[macs2]
[reg]
[seqpos]
[species], [1], [2], [3]
[tool]
chrom_len, [1]
conservation, [1]
cont
db
dhs, [1]
dist
extsize
factor
fdr
geneTable, [1]
genome_dir, [1]
genome_index, [1], [2]
id, [1]
keep_dup
macs2
mdscan_top_peaks
mdscan_width
mdseqpos
output, [1]
peaks
peaks[forconservation]
peaks[forreg]
pvalue_cutoff
seqpos_mdscan_top_peaks_refine
species
time
treat
type[forconservation]
type[formacs2]
user
velcro, [1]
width, [1]

G

geneTable
genome_dir
genome_index, [1]

I

id

M

macs2() (chilin2.modules.macs.dc method)

O

output

P

PythonCommand (class in samflow.command)

S

samflow (module)
ShellCommand (class in samflow.command)

V

velcro

W

Workflow (class in samflow.workflow)