netZooPy
stable
Installation guide
Tutorials
Command Line Interface
The Animals (API)
Changelog
netZooPy
Index
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Index
Symbols
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_
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A
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B
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C
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D
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E
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I
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L
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M
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N
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P
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Q
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R
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S
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T
Symbols
--alpha
netzoopy-lioness command line option
netzoopy-panda command line option
--as_adjacency
netzoopy-lioness command line option
netzoopy-panda command line option
--com_num
netzoopy-condor command line option
--computing
netzoopy-lioness command line option
netzoopy-panda command line option
--confidence
netzoopy-bonobo command line option
--delta
netzoopy-bonobo command line option
--delta_qmin
netzoopy-condor command line option
--el
netzoopy-lioness command line option
--end
netzoopy-lioness command line option
netzoopy-panda command line option
--expression
netzoopy-lioness command line option
netzoopy-panda command line option
--expression_file
netzoopy-bonobo command line option
--fmt
netzoopy-lioness command line option
--header
netzoopy-condor command line option
--ignore_final
netzoopy-lioness command line option
--index_col
netzoopy-condor command line option
--initial_method
netzoopy-condor command line option
--initial_project
netzoopy-condor command line option
--keep_expr
netzoopy-panda command line option
--keep_in_memory
netzoopy-bonobo command line option
--mode_process
netzoopy-lioness command line option
netzoopy-panda command line option
--motif
netzoopy-lioness command line option
netzoopy-panda command line option
--ncores
netzoopy-lioness command line option
--network_file
netzoopy-condor command line option
--old_compatible
netzoopy-lioness command line option
netzoopy-panda command line option
--out
netzoopy-panda command line option
--out-lioness
netzoopy-lioness command line option
--out-panda
netzoopy-lioness command line option
--output_folder
netzoopy-bonobo command line option
--output_format
netzoopy-bonobo command line option
--output_type
netzoopy-lioness command line option
--panda_end
netzoopy-lioness command line option
--panda_start
netzoopy-lioness command line option
--ppi
netzoopy-lioness command line option
netzoopy-panda command line option
--precision
netzoopy-bonobo command line option
netzoopy-lioness command line option
netzoopy-panda command line option
--reg_output
netzoopy-condor command line option
--resolution
netzoopy-condor command line option
--rm_missing
netzoopy-lioness command line option
netzoopy-panda command line option
--sample_names
netzoopy-bonobo command line option
--save_memory
netzoopy-panda command line option
--save_pvals
netzoopy-bonobo command line option
--save_single_lioness
netzoopy-lioness command line option
--save_tmp
netzoopy-lioness command line option
netzoopy-panda command line option
--sep
netzoopy-condor command line option
--sparsify
netzoopy-bonobo command line option
--start
netzoopy-lioness command line option
netzoopy-panda command line option
--subset_names
netzoopy-lioness command line option
--subset_numbers
netzoopy-lioness command line option
--tar_output
netzoopy-condor command line option
--with_header
netzoopy-lioness command line option
netzoopy-panda command line option
-e
netzoopy-bonobo command line option
netzoopy-lioness command line option
netzoopy-panda command line option
-m
netzoopy-lioness command line option
netzoopy-panda command line option
-n
netzoopy-condor command line option
-o
netzoopy-panda command line option
-ol
netzoopy-lioness command line option
-op
netzoopy-lioness command line option
-p
netzoopy-lioness command line option
netzoopy-panda command line option
_
__create_plot() (netZooPy.panda.analyze_panda.AnalyzePanda method)
(netZooPy.panda.panda.Panda method)
(netZooPy.puma.puma.Puma method)
__lioness_loop() (netZooPy.lioness.lioness.Lioness method)
__lioness_to_disk() (netZooPy.lioness.lioness.Lioness method)
__par_lioness_loop (netZooPy.lioness.lioness.Lioness attribute)
__pearson_results_data_frame() (netZooPy.panda.panda.Panda method)
(netZooPy.puma.puma.Puma method)
__remove_missing() (netZooPy.panda.panda.Panda method)
(netZooPy.puma.puma.Puma method)
__shape_plot_network() (netZooPy.panda.analyze_panda.AnalyzePanda method)
(netZooPy.panda.panda.Panda method)
(netZooPy.puma.puma.Puma method)
_bonobo_loop() (netZooPy.ligress.bonobo.Bonobo method)
_normalize_network() (netZooPy.lioness.lioness.Lioness method)
(netZooPy.panda.panda.Panda method)
(netZooPy.puma.puma.Puma method)
_prepare_expression() (netZooPy.ligress.bonobo.Bonobo method)
A
AnalyzeLioness (class in netZooPy.lioness.analyze_lioness)
AnalyzePanda (class in netZooPy.panda.analyze_panda)
B
binomial_dist() (in module netZooPy.sambar)
bipartite_modularity() (netZooPy.condor.condor.condor_object method)
Bonobo (class in netZooPy.ligress.bonobo)
brim() (netZooPy.condor.condor.condor_object method)
C
clustering() (in module netZooPy.sambar)
compute_bonobo() (in module netZooPy.ligress.bonobo)
condor_object (class in netZooPy.condor.condor)
convertgmt() (in module netZooPy.sambar)
corgenelength() (in module netZooPy.sambar)
D
desparsify() (in module netZooPy.sambar)
E
export_lioness_table() (netZooPy.lioness.lioness.Lioness method)
I
initial_community() (netZooPy.condor.condor.condor_object method)
L
Lioness (class in netZooPy.lioness.lioness)
M
main() (in module netZooPy.lioness.run_lioness)
(in module netZooPy.panda.run_panda)
matrices() (netZooPy.condor.condor.condor_object method)
N
netzoopy-bonobo command line option
--confidence
--delta
--expression_file
--keep_in_memory
--output_folder
--output_format
--precision
--sample_names
--save_pvals
--sparsify
-e
netzoopy-condor command line option
--com_num
--delta_qmin
--header
--index_col
--initial_method
--initial_project
--network_file
--reg_output
--resolution
--sep
--tar_output
-n
netzoopy-lioness command line option
--alpha
--as_adjacency
--computing
--el
--end
--expression
--fmt
--ignore_final
--mode_process
--motif
--ncores
--old_compatible
--out-lioness
--out-panda
--output_type
--panda_end
--panda_start
--ppi
--precision
--rm_missing
--save_single_lioness
--save_tmp
--start
--subset_names
--subset_numbers
--with_header
-e
-m
-ol
-op
-p
netzoopy-panda command line option
--alpha
--as_adjacency
--computing
--end
--expression
--keep_expr
--mode_process
--motif
--old_compatible
--out
--ppi
--precision
--rm_missing
--save_memory
--save_tmp
--start
--with_header
-e
-m
-o
-p
P
Panda (class in netZooPy.panda.panda)
panda_loop() (netZooPy.lioness.lioness.Lioness method)
(netZooPy.panda.panda.Panda method)
prepare_expression() (in module netZooPy.ligress.io)
processData() (netZooPy.lioness.lioness.Lioness method)
(netZooPy.panda.panda.Panda method)
Puma (class in netZooPy.puma.puma)
puma_loop() (netZooPy.puma.puma.Puma method)
Q
qscores() (netZooPy.condor.condor.condor_object method)
R
return_panda_indegree() (netZooPy.lioness.lioness.Lioness method)
(netZooPy.panda.panda.Panda method)
return_panda_outdegree() (netZooPy.lioness.lioness.Lioness method)
(netZooPy.panda.panda.Panda method)
return_puma_indegree() (netZooPy.puma.puma.Puma method)
return_puma_outdegree() (netZooPy.puma.puma.Puma method)
run_bonobo() (netZooPy.ligress.bonobo.Bonobo method)
run_condor() (in module netZooPy.condor)
S
sambar() (in module netZooPy.sambar)
save_lioness_results() (netZooPy.lioness.lioness.Lioness method)
save_panda_results() (netZooPy.lioness.lioness.Lioness method)
(netZooPy.panda.panda.Panda method)
save_puma_results() (netZooPy.puma.puma.Puma method)
T
top_network_plot() (netZooPy.lioness.analyze_lioness.AnalyzeLioness method)
(netZooPy.lioness.lioness.Lioness method)
(netZooPy.panda.analyze_panda.AnalyzePanda method)
(netZooPy.panda.panda.Panda method)
(netZooPy.puma.puma.Puma method)
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