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Identifier Index
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A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X Y Z
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]
A
add_nonfunctional_factor()
(in
KnockoutTranssysProgram
)
adjacency_matrix_scorefunc()
(in
transdisrupt
)
arrtool
add_regulon()
(in
RegStructTranssys
)
adjust_histogram_parameters()
(in
RTAControlParameters
)
adjacency_matrix()
(in
transdisrupt
)
arrowLine()
(in
BindingSite
)
B
baseToInt()
(in
transdecode
)
BindingSite
(in
transdecode
)
bindingEnergy()
(in
DNABinder
)
bindingSite()
(in
DNABinder
)
C
choose_perturbed_factors()
(in
RegStructTranssys
)
cmp_by_score()
(in
arrtool
)
complete_arrtool_basename()
(in
RTAControlParameters
)
cluster()
(in
RegulonDescriptor
)
column_type()
(in
MicroarrayData
)
create_disruption_network()
(in
transdisrupt
)
cluster_size()
(in
ClusterNode
)
complete()
(in
RTAControlParameters
)
ClusterNode
(in
regstruct
)
complete_array_fname()
(in
RTAControlParameters
)
D
decode()
(in
DNABinder
)
DNABinder
(in
transdecode
)
dot_fname()
(in
RTAControlParameters
)
decode_transsys()
(in
TranssysDNADecoder
)
do_knockout()
(in
KnockoutTranssysProgram
)
E
environment_perturber()
(in
RTAControlParameters
)
ExperimentSpec
(in
arrtool
)
ExponentialReplacementPerturber
(in
regstruct
)
ErrorLogger
(in
transdisrupt
)
experimentspecs_fname()
(in
RTAControlParameters
)
ExpressionSimilarityMatrix
(in
transdisrupt
)
experiment_plots()
(in
MicroarrayData
)
ExpGaussPerturber
(in
regstruct
)
F
factor_gene_dictionary()
(in
ExpressionSimilarityMatrix
)
fill_all()
(in
ExpressionSimilarityMatrix
)
find_binding_sites()
(in
transdecode
)
G
gene_factor_dictionary()
(in
ExpressionSimilarityMatrix
)
get_element()
(in
ExpressionSimilarityMatrix
)
get_namevalue()
(in
regstruct
)
gene_factor_dictionary()
(in
transdisrupt
)
get_fname()
(in
ExpressionSimilarityMatrix
)
gnu_comparison()
(in
ExpressionSimilarityMatrix
)
gene_plot_data()
(in
ExperimentSpec
)
get_fnamelist()
(in
ExpressionSimilarityMatrix
)
gnuplot_command_fname()
(in
RTAControlParameters
)
genegroup_line()
(in
RegulonDescriptor
)
get_gnamelist()
(in
ExpressionSimilarityMatrix
)
genegroups_fname()
(in
RTAControlParameters
)
get_index()
(in
ExpressionSimilarityMatrix
)
I
identity_perturber()
(in
transdisrupt
)
K
knockout_concentration_matrix()
(in
transdisrupt
)
knockout_concentration_matrix_lsys()
(in
transdisrupt
)
KnockoutTranssysProgram
(in
transdisrupt
)
L
link_scorefunc()
(in
transdisrupt
)
logratio_matrix()
(in
transdisrupt
)
M
max_score()
(in
DNABinder
)
message()
(in
ErrorLogger
)
MicroarrayData
(in
arrtool
)
N
nonperturbed_array_fname()
(in
RTAControlParameters
)
nonperturbed_euclidean_average_fname()
(in
RTAControlParameters
)
normalisedColumn()
(in
transdecode
)
nonperturbed_arrtool_basename()
(in
RTAControlParameters
)
nonperturbed_euclidean_complete_fname()
(in
RTAControlParameters
)
num_columns()
(in
ExperimentSpec
)
nonperturbed_cluster()
(in
RTAControlParameters
)
nonperturbed_euclidean_single_fname()
(in
RTAControlParameters
)
num_columns()
(in
MicroarrayData
)
nonperturbed_clustertree_basename()
(in
RTAControlParameters
)
nonperturbed_factor_list()
(in
RTAControlParameters
)
num_rows()
(in
MicroarrayData
)
nonperturbed_clustertree_fname()
(in
RTAControlParameters
)
nonperturbed_regnet_factor_list()
(in
RTAControlParameters
)
O
overlaps()
(in
transdisrupt
)
P
parse()
(in
RTAControlParameters
)
parse_cluster()
(in
regstruct
)
pathscore_matrix()
(in
transdisrupt
)
parse()
(in
RegulonDescriptor
)
parse_int_csv()
(in
regstruct
)
promoterArea()
(in
RawDNAGene
)
parse()
(in
TranssysDNADecoder
)
parse_string_csv()
(in
regstruct
)
R
r_fname()
(in
RTAControlParameters
)
regcontrol_factor_name()
(in
regstruct
)
regulon_name()
(in
regstruct
)
RawDNAGene
(in
transdecode
)
regcontrol_gene_name()
(in
regstruct
)
RegulonDescriptor
(in
regstruct
)
rawDNAGenes()
(in
TranssysDNADecoder
)
regnet_factors()
(in
RegStructTranssys
)
replace_none()
(in
ExpressionSimilarityMatrix
)
rawSequence()
(in
RawDNAGene
)
regstruct
return_as_list()
(in
ExpressionSimilarityMatrix
)
read_file()
(in
MicroarrayData
)
RegStructTranssys
(in
regstruct
)
RTAControlParameters
(in
regstruct
)
reconstructed_adjacency_matrix()
(in
transdisrupt
)
regulation_index()
(in
MicroarrayData
)
run_plottree()
(in
RTAControlParameters
)
referencestate_concentration_matrix()
(in
transdisrupt
)
regulation_index_list()
(in
MicroarrayData
)
run_r()
(in
RTAControlParameters
)
S
savefile_magic
(in
TranssysDNADecoder
)
set_ultrametric_distance()
(in
ClusterNode
)
struct_gene_name()
(in
regstruct
)
score_matrix()
(in
transdisrupt
)
setGeneEndRE()
(in
TranssysDNADecoder
)
struct_protein_name()
(in
regstruct
)
set_ancestor()
(in
ClusterNode
)
setGeneStartRE()
(in
TranssysDNADecoder
)
set_element()
(in
ExpressionSimilarityMatrix
)
setup_gene_dict()
(in
MicroarrayData
)
T
transdecode
transsys_fname()
(in
RTAControlParameters
)
treelist_fname()
(in
RTAControlParameters
)
transdisrupt
TranssysDNADecoder
(in
transdecode
)
U
undo_knockout()
(in
KnockoutTranssysProgram
)
uniform_cmp()
(in
transdisrupt
)
UniformReplacementPerturber
(in
regstruct
)
W
write()
(in
RTAControlParameters
)
write_genegroups()
(in
RegStructTranssys
)
write_nonperturbed_cluster()
(in
RTAControlParameters
)
write()
(in
TranssysDNADecoder
)
write_gnuplot_file()
(in
ExperimentSpec
)
write_r_commands()
(in
RTAControlParameters
)
write_genegroups()
(in
RTAControlParameters
)
write_gnuplot_file()
(in
MicroarrayData
)
_
__call__()
(in
ExpGaussPerturber
)
__init__()
(in
RegStructTranssys
)
__init__()
(in
KnockoutTranssysProgram
)
__call__()
(in
ExponentialReplacementPerturber
)
__init__()
(in
RegulonDescriptor
)
__package__
(in
arrtool
)
__call__()
(in
UniformReplacementPerturber
)
__init__()
(in
UniformReplacementPerturber
)
__str__()
(in
ClusterNode
)
__init__()
(in
ExperimentSpec
)
__init__()
(in
BindingSite
)
__str__()
(in
RegulonDescriptor
)
__init__()
(in
MicroarrayData
)
__init__()
(in
DNABinder
)
__str__()
(in
DNABinder
)
__init__()
(in
ClusterNode
)
__init__()
(in
RawDNAGene
)
__str__()
(in
TranssysDNADecoder
)
__init__()
(in
ExpGaussPerturber
)
__init__()
(in
TranssysDNADecoder
)
__str__()
(in
ExpressionSimilarityMatrix
)
__init__()
(in
ExponentialReplacementPerturber
)
__init__()
(in
ErrorLogger
)
__init__()
(in
RTAControlParameters
)
__init__()
(in
ExpressionSimilarityMatrix
)
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