Index

B

bam2chicago() (CHiC.tool.bam2chicago_tool.bam2chicagoTool method)

bam2chicagoTool (class in CHiC.tool.bam2chicago_tool)

C

chicago() (CHiC.tool.run_chicago.ChicagoTool method)

ChicagoTool (class in CHiC.tool.run_chicago)

D

digest_genome() (CHiC.tool.hicup_tool.hicup method)

G

get_chicago_params() (CHiC.tool.run_chicago.ChicagoTool static method)

get_design_params() (CHiC.tool.makeDesignFiles.makeDesignFilesTool static method) get_hicup_params() (CHiC.tool.hicup_tool.hicup static method)

H

hicup (class in CHiC.tool.hicup_tool)

hicup_alig_filt() (CHiC.tool.hicup_tool.hicup method)

M

makeDesignFiles() (CHiC.tool.makeDesignFiles.makeDesignFilesTool method)

makeDesignFilesTool (class in CHiC.tool.makeDesignFiles)

P

process_bam2chicago (class in process_bam2chicago_tool) process_bam2chicago_tool (module) process_design (class in process_design) (module)

process_hicup (class in process_hicup) (module) process_run_chicago (class in process_run_chicago) (module)

R

run() (CHiC.tool.bam2chicago_tool.bam2chicagoTool method) (CHiC.tool.hicup_tool.hicup method) (CHiC.tool.makeDesignFiles.makeDesignFilesTool method) (CHiC.tool.run_chicago.ChicagoTool method) (process_bam2chicago_tool.process_bam2chicago method) (process_design.process_design method) (process_hicup.process_hicup method) (process_run_chicago.process_run_chicago method)

S

sort_chicago() (CHiC.tool.bam2chicago_tool.bam2chicagoTool method)

T

tool (module)

U

untar_chinput() (CHiC.tool.run_chicago.ChicagoTool static method)

untar_hicup_out() (CHiC.tool.bam2chicago_tool.bam2chicagoTool static method) untar_index() (CHiC.tool.hicup_tool.hicup method)