Index

Symbols

--activation-threshold drug2ways-combine command line option drug2ways-optimize command line option --combination-length drug2ways-combine command line option --drug-search-bel drug2ways-explore command line option --fmt drug2ways-combine command line option drug2ways-explore command line option drug2ways-optimize command line option drug2ways-pathway-analysis command line option drug2ways-validate-with-data command line option --graph drug2ways-combine command line option drug2ways-explore command line option drug2ways-optimize command line option drug2ways-pathway-analysis command line option drug2ways-validate-with-data command line option --lmax drug2ways-combine command line option drug2ways-explore command line option drug2ways-optimize command line option drug2ways-pathway-analysis command line option drug2ways-validate-with-data command line option --log drug2ways-combine command line option drug2ways-explore command line option drug2ways-optimize command line option drug2ways-pathway-analysis command line option drug2ways-validate-with-data command line option --name drug2ways-explore command line option drug2ways-validate-with-data command line option --output drug2ways-combine command line option drug2ways-explore command line option drug2ways-optimize command line option drug2ways-pathway-analysis command line option drug2ways-validate-with-data command line option --simple drug2ways-combine command line option drug2ways-explore command line option drug2ways-optimize command line option drug2ways-pathway-analysis command line option drug2ways-validate-with-data command line option --sources drug2ways-combine command line option drug2ways-explore command line option drug2ways-optimize command line option drug2ways-pathway-analysis command line option --target drug2ways-validate-with-data command line option, [1]

--targets drug2ways-combine command line option drug2ways-explore command line option drug2ways-optimize command line option drug2ways-pathway-analysis command line option --time drug2ways-explore command line option -a drug2ways-combine command line option drug2ways-optimize command line option -c drug2ways-combine command line option -d drug2ways-explore command line option -f drug2ways-combine command line option drug2ways-explore command line option drug2ways-optimize command line option drug2ways-pathway-analysis command line option drug2ways-validate-with-data command line option -g drug2ways-combine command line option drug2ways-explore command line option drug2ways-optimize command line option drug2ways-pathway-analysis command line option drug2ways-validate-with-data command line option -l drug2ways-combine command line option, [1] drug2ways-explore command line option, [1] drug2ways-optimize command line option, [1] drug2ways-pathway-analysis command line option, [1] drug2ways-validate-with-data command line option, [1] -n drug2ways-explore command line option drug2ways-validate-with-data command line option -o drug2ways-combine command line option drug2ways-explore command line option drug2ways-optimize command line option drug2ways-pathway-analysis command line option drug2ways-validate-with-data command line option -s drug2ways-combine command line option drug2ways-explore command line option drug2ways-optimize command line option drug2ways-pathway-analysis command line option -t drug2ways-combine command line option drug2ways-explore command line option, [1] drug2ways-optimize command line option drug2ways-pathway-analysis command line option drug2ways-validate-with-data command line option, [1]

B

BEL (in module drug2ways.constants)

BEL_PICKLE (in module drug2ways.constants)

C

compute_all_paths_multitarget() (in module drug2ways.graph_traversal)

compute_all_paths_multitarget_dict() (in module drug2ways.graph_traversal) CSV (in module drug2ways.constants)

D

DEFAULT_DRUG2WAYS_DIR (in module drug2ways.constants) download_pathway() (in module drug2ways.constants) drug2ways-combine command line option --activation-threshold --combination-length --fmt --graph --lmax --log --output --simple --sources --targets -a -c -f -g -l, [1] -o -s -t drug2ways-explore command line option --drug-search-bel --fmt --graph --lmax --log --name --output --simple --sources --targets --time -d -f -g -l, [1] -n -o -s -t, [1] drug2ways-optimize command line option --activation-threshold --fmt --graph --lmax --log --output --simple --sources --targets -a -f -g -l, [1] -o -s -t

drug2ways-pathway-analysis command line option --fmt --graph --lmax --log --output --simple --sources --targets -f -g -l, [1] -o -s -t drug2ways-validate-with-data command line option --fmt --graph --lmax --log --name --output --simple --target, [1] -f -g -l, [1] -n -o -t, [1] drug2ways.alternative_graph_traversal module drug2ways.constants module drug2ways.graph_traversal module

E

EDGE_LIST (in module drug2ways.constants) EMOJI (in module drug2ways.constants)

ensure_genesets() (in module drug2ways.constants) ensure_output_dirs() (in module drug2ways.constants) enumerate_paths() (in module drug2ways.alternative_graph_traversal)

F

FORMAT_SEPARATOR_MAPPING (in module drug2ways.constants)

FORMATS (in module drug2ways.constants)

G

GML (in module drug2ways.constants)

GRAPHML (in module drug2ways.constants)

M

module drug2ways.alternative_graph_traversal drug2ways.constants drug2ways.graph_traversal

N

NODE_LINK_JSON (in module drug2ways.constants)

R

RELATION (in module drug2ways.constants)

S

SOURCE (in module drug2ways.constants)

T

TARGET (in module drug2ways.constants)

TSV (in module drug2ways.constants)