tmtk
0.5.5
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Data templates
tmtk
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B
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C
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D
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E
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F
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G
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H
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I
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J
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
A
add_datafile() (tmtk.clinical.Clinical method)
add_node() (tmtk.arborist.jstreecontrol.ConceptTree method)
add_params() (tmtk.params.Params.Params method)
all_files (tmtk.Study attribute)
all_variables (tmtk.clinical.Clinical attribute)
allowed_header (tmtk.highdim.CopyNumberVariation.CopyNumberVariation attribute)
(tmtk.highdim.ReadCounts.ReadCounts attribute)
ancestors (tmtk.utils.mappings.Mappings attribute)
annotation_data_types (tmtk.utils.mappings.Mappings attribute)
annotation_files (tmtk.annotation.Annotations.Annotations attribute)
(tmtk.Study attribute)
annotation_marker_types (tmtk.utils.mappings.Mappings attribute)
AnnotationBase (class in tmtk.annotation.AnnotationBase)
AnnotationParams (class in tmtk.params.AnnotationParams)
Annotations (class in tmtk.annotation.Annotations)
append_from_datafile() (tmtk.clinical.ColumnMapping method)
apply_blueprint() (tmtk.clinical.Clinical method)
(tmtk.Study method)
(tmtk.tags.Tags.MetaDataTags method)
ArboristException
B
biomarkers (tmtk.annotation.ChromosomalRegions.ChromosomalRegions attribute)
(tmtk.annotation.MicroarrayAnnotation.MicroarrayAnnotation attribute)
(tmtk.annotation.MirnaAnnotation.MirnaAnnotation attribute)
(tmtk.annotation.ProteomicsAnnotation.ProteomicsAnnotation attribute)
blob (tmtk.utils.mappings.Mappings attribute)
BlueprintException
build_index() (tmtk.clinical.ColumnMapping method)
(tmtk.clinical.WordMapping method)
C
call_boris() (in module tmtk.arborist.common)
(tmtk.Study method)
cat_cd (tmtk.utils.mappings.Mappings attribute)
cat_cd_s (tmtk.utils.mappings.Mappings attribute)
category_code (tmtk.clinical.Variable attribute)
ChromosomalRegions (class in tmtk.annotation.ChromosomalRegions)
ClassError
clean_for_namespace() (in module tmtk.utils.Generic)
Clinical (class in tmtk.clinical)
clinical_files (tmtk.clinical.Clinical attribute)
(tmtk.Study attribute)
ClinicalParams (class in tmtk.params.ClinicalParams)
col_num (tmtk.utils.mappings.Mappings attribute)
col_num_s (tmtk.utils.mappings.Mappings attribute)
column_map_data (tmtk.clinical.Variable attribute)
column_map_diff() (in module tmtk.utils.Generic)
column_mapping_file (tmtk.arborist.jstreecontrol.ConceptTree attribute)
column_mapping_header (tmtk.utils.mappings.Mappings attribute)
column_mapping_s (tmtk.utils.mappings.Mappings attribute)
column_type (tmtk.clinical.Variable attribute)
(tmtk.utils.mappings.Mappings attribute)
ColumnMapping (class in tmtk.clinical)
(tmtk.clinical.Clinical attribute)
concept_code (tmtk.clinical.Variable attribute)
concept_path (tmtk.clinical.Variable attribute)
concept_tree (tmtk.Study attribute)
concept_tree_json (tmtk.Study attribute)
concept_tree_to_clipboard() (tmtk.Study method)
concept_type (tmtk.utils.mappings.Mappings attribute)
concept_type_s (tmtk.utils.mappings.Mappings attribute)
ConceptNode (class in tmtk.arborist.jstreecontrol)
ConceptTree (class in tmtk.arborist.jstreecontrol)
CopyNumberVariation (class in tmtk.highdim.CopyNumberVariation)
create_clinical() (tmtk.Study method)
create_concept_tree() (in module tmtk.arborist.jstreecontrol)
create_df() (tmtk.clinical.ColumnMapping method)
(tmtk.clinical.WordMapping method)
(tmtk.tags.Tags.MetaDataTags static method)
create_params() (tmtk.params.Params.Params static method)
create_study() (in module tmtk.toolbox.wizard)
create_study_from_templates() (in module tmtk.toolbox)
create_tree_from_clinical() (in module tmtk.arborist.jstreecontrol)
create_tree_from_study() (in module tmtk.arborist.jstreecontrol)
D
data_label (tmtk.clinical.Variable attribute)
(tmtk.utils.mappings.Mappings attribute)
data_label_s (tmtk.utils.mappings.Mappings attribute)
DataFile (class in tmtk.clinical)
DatatypeError
default() (tmtk.arborist.jstreecontrol.MyEncoder method)
df (tmtk.utils.filebase.FileBase attribute)
df2file() (in module tmtk.utils.Generic)
df_has_changed (tmtk.utils.filebase.FileBase attribute)
df_value (tmtk.utils.mappings.Mappings attribute)
df_value_s (tmtk.utils.mappings.Mappings attribute)
docslink (tmtk.params.ClinicalParams.ClinicalParams attribute)
(tmtk.params.HighDimParams.HighDimParams attribute)
(tmtk.params.StudyParams.StudyParams attribute)
E
end_date (tmtk.clinical.Variable attribute)
ensure_metadata() (tmtk.Study method)
Expression (class in tmtk.highdim.Expression)
EXT_PATH_DELIM (tmtk.utils.mappings.Mappings attribute)
F
file2df() (in module tmtk.utils.Generic)
FileBase (class in tmtk.utils.filebase)
filename (tmtk.utils.mappings.Mappings attribute)
filename_s (tmtk.utils.mappings.Mappings attribute)
files_with_changes() (tmtk.Study method)
filtered_variables (tmtk.clinical.Clinical attribute)
find_annotation() (tmtk.Study method)
find_fully_unique_columns() (in module tmtk.utils.Generic)
find_params_for_datatype() (tmtk.Study method)
find_variables_by_label() (tmtk.clinical.Clinical method)
fix_everything() (in module tmtk.utils.Generic)
forced_categorical (tmtk.clinical.Variable attribute)
G
generate_chromosomal_regions_file() (in module tmtk.toolbox.generate_chromosomal_regions_file)
get_annotations() (tmtk.utils.mappings.Mappings static method)
get_child() (tmtk.arborist.jstreecontrol.JSNode method)
get_concept_path() (tmtk.clinical.ColumnMapping method)
get_concept_paths (tmtk.highdim.SampleMapping.SampleMapping attribute)
get_datafile() (tmtk.clinical.Clinical method)
get_dimensions() (tmtk.Study method)
get_highdim() (tmtk.utils.mappings.Mappings static method)
get_instance_url() (in module tmtk.arborist.connect_to_baas)
get_json_from_baas() (in module tmtk.arborist.connect_to_baas)
get_object_from_params_path() (tmtk.Study method)
get_objects() (tmtk.Study method)
get_params() (tmtk.utils.mappings.Mappings static method)
get_patients() (tmtk.clinical.Clinical method)
get_tags() (tmtk.tags.Tags.MetaDataTags method)
get_trial_visits() (tmtk.clinical.Clinical method)
get_variable() (tmtk.clinical.Clinical method)
get_word_map() (tmtk.clinical.WordMapping method)
H
header (tmtk.clinical.Variable attribute)
(tmtk.utils.filebase.FileBase attribute)
high_dim_files (tmtk.highdim.HighDim.HighDim attribute)
(tmtk.Study attribute)
high_dim_paths (tmtk.arborist.jstreecontrol.ConceptTree attribute)
HighDim (class in tmtk.highdim.HighDim)
HighDimBase (class in tmtk.highdim.HighDimBase)
HighDimParams (class in tmtk.params.HighDimParams)
I
ids (tmtk.clinical.ColumnMapping attribute)
included_datafiles (tmtk.clinical.ColumnMapping attribute)
(tmtk.clinical.WordMapping attribute)
invalid_paths (tmtk.tags.Tags.MetaDataTags attribute)
is_empty (tmtk.clinical.Variable attribute)
is_in_wordmap (tmtk.clinical.Variable attribute)
is_not_a_value() (in module tmtk.utils.Generic)
is_numeric (tmtk.clinical.Variable attribute)
is_numeric_in_datafile (tmtk.clinical.Variable attribute)
is_viable() (tmtk.params.AnnotationParams.AnnotationParams method)
(tmtk.params.HighDimParams.HighDimParams method)
(tmtk.params.TagsParams.TagsParams method)
J
JSNode (class in tmtk.arborist.jstreecontrol)
json_data (tmtk.arborist.jstreecontrol.JSTree attribute)
json_data() (tmtk.arborist.jstreecontrol.JSNode method)
json_data_string (tmtk.arborist.jstreecontrol.JSTree attribute)
json_url() (in module tmtk.arborist.connect_to_baas)
JSTree (class in tmtk.arborist.jstreecontrol)
jstree (tmtk.arborist.jstreecontrol.ConceptTree attribute)
L
launch_arborist_gui() (in module tmtk.arborist.common)
load_to (tmtk.annotation.AnnotationBase.AnnotationBase attribute)
(tmtk.Study attribute)
(tmtk.clinical.Clinical attribute)
(tmtk.highdim.HighDimBase.HighDimBase attribute)
(tmtk.tags.Tags.MetaDataTags attribute)
login_url() (in module tmtk.arborist.connect_to_baas)
M
magic_5 (tmtk.utils.mappings.Mappings attribute)
magic_5_s (tmtk.utils.mappings.Mappings attribute)
magic_6_s (tmtk.utils.mappings.Mappings attribute)
mandatory (tmtk.params.AnnotationParams.AnnotationParams attribute)
(tmtk.params.ClinicalParams.ClinicalParams attribute)
(tmtk.params.HighDimParams.HighDimParams attribute)
(tmtk.params.StudyParams.StudyParams attribute)
(tmtk.params.TagsParams.TagsParams attribute)
map_index_to_region_ids() (in module tmtk.toolbox.remap_chromosomal_regions)
map_value (tmtk.utils.mappings.Mappings attribute)
map_value_s (tmtk.utils.mappings.Mappings attribute)
mapped_values (tmtk.clinical.Variable attribute)
Mappings (class in tmtk.utils.mappings)
marker_type (tmtk.annotation.AnnotationBase.AnnotationBase attribute)
max (tmtk.clinical.Variable attribute)
md5() (in module tmtk.utils.Generic)
merge_two_dicts() (in module tmtk.utils.Generic)
MetaDataTags (class in tmtk.tags.Tags)
MicroarrayAnnotation (class in tmtk.annotation.MicroarrayAnnotation)
min (tmtk.clinical.Variable attribute)
Mirna (class in tmtk.highdim.Mirna)
MirnaAnnotation (class in tmtk.annotation.MirnaAnnotation)
modifier_cd (tmtk.utils.mappings.Mappings attribute)
modifier_code (tmtk.clinical.Variable attribute)
modifier_path (tmtk.utils.mappings.Mappings attribute)
modifiers (tmtk.clinical.Variable attribute)
modifiers_header (tmtk.utils.mappings.Mappings attribute)
MyEncoder (class in tmtk.arborist.jstreecontrol)
N
name (tmtk.utils.filebase.FileBase attribute)
name_char (tmtk.utils.mappings.Mappings attribute)
O
ontology_code (tmtk.utils.mappings.Mappings attribute)
ontology_header (tmtk.utils.mappings.Mappings attribute)
optional (tmtk.params.AnnotationParams.AnnotationParams attribute)
(tmtk.params.ClinicalParams.ClinicalParams attribute)
(tmtk.params.HighDimParams.HighDimParams attribute)
(tmtk.params.StudyParams.StudyParams attribute)
(tmtk.params.TagsParams.TagsParams attribute)
P
Params (class in tmtk.params.Params)
params (tmtk.clinical.Clinical attribute)
path_changes() (tmtk.clinical.ColumnMapping method)
path_converter() (in module tmtk.utils.Generic)
PATH_DELIM (tmtk.utils.mappings.Mappings attribute)
path_id_dict (tmtk.clinical.ColumnMapping attribute)
path_join() (in module tmtk.utils.Generic)
PathError
platform (tmtk.highdim.SampleMapping.SampleMapping attribute)
pretty() (tmtk.arborist.jstreecontrol.JSTree method)
Proteomics (class in tmtk.highdim.Proteomics)
ProteomicsAnnotation (class in tmtk.annotation.ProteomicsAnnotation)
publish_to_baas() (in module tmtk.arborist.connect_to_baas)
(tmtk.Study method)
R
ReadCounts (class in tmtk.highdim.ReadCounts)
reference_column (tmtk.clinical.Variable attribute)
remap_chromosomal_regions() (in module tmtk.toolbox.remap_chromosomal_regions)
remap_to() (tmtk.highdim.CopyNumberVariation.CopyNumberVariation method)
(tmtk.highdim.ReadCounts.ReadCounts method)
RESERVED_KEYWORDS (tmtk.clinical.ColumnMapping attribute)
ReservedKeywordException
return_mean() (in module tmtk.toolbox.remap_chromosomal_regions)
S
sample_mapping_files (tmtk.highdim.HighDim.HighDim attribute)
(tmtk.Study attribute)
SampleMapping (class in tmtk.highdim.SampleMapping)
samples (tmtk.highdim.CopyNumberVariation.CopyNumberVariation attribute)
(tmtk.highdim.Expression.Expression attribute)
(tmtk.highdim.Mirna.Mirna attribute)
(tmtk.highdim.Proteomics.Proteomics attribute)
(tmtk.highdim.ReadCounts.ReadCounts attribute)
(tmtk.highdim.SampleMapping.SampleMapping attribute)
save() (tmtk.utils.filebase.FileBase method)
security_required (tmtk.Study attribute)
select_row() (tmtk.clinical.ColumnMapping method)
set_column_type() (tmtk.clinical.ColumnMapping method)
set_concept_code() (tmtk.clinical.ColumnMapping method)
set_concept_path() (tmtk.clinical.ColumnMapping method)
set_reference_column() (tmtk.clinical.ColumnMapping method)
set_word_map() (tmtk.clinical.WordMapping method)
show_changes() (tmtk.clinical.Clinical method)
slice_path() (tmtk.highdim.SampleMapping.SampleMapping method)
start_date (tmtk.clinical.Variable attribute)
start_session() (in module tmtk.arborist.connect_to_baas)
Study (class in tmtk)
study_blob (tmtk.Study attribute)
study_id (tmtk.highdim.SampleMapping.SampleMapping attribute)
(tmtk.Study attribute)
study_name (tmtk.Study attribute)
StudyParams (class in tmtk.params.StudyParams)
subj_id (tmtk.clinical.Variable attribute)
subj_id_columns (tmtk.clinical.ColumnMapping attribute)
summarise() (in module tmtk.utils.Generic)
T
tabs_in_first_line() (tmtk.utils.filebase.FileBase method)
tag_files (tmtk.Study attribute)
tag_paths (tmtk.tags.Tags.MetaDataTags attribute)
tags_description (tmtk.utils.mappings.Mappings attribute)
tags_file (tmtk.arborist.jstreecontrol.ConceptTree attribute)
tags_header (tmtk.utils.mappings.Mappings attribute)
tags_node_name (tmtk.utils.mappings.Mappings attribute)
tags_path (tmtk.utils.mappings.Mappings attribute)
tags_title (tmtk.utils.mappings.Mappings attribute)
tags_weight (tmtk.utils.mappings.Mappings attribute)
TagsParams (class in tmtk.params.TagsParams)
term_label (tmtk.utils.mappings.Mappings attribute)
tmtk (module)
tmtk.annotation.AnnotationBase (module)
tmtk.annotation.Annotations (module)
tmtk.annotation.ChromosomalRegions (module)
tmtk.annotation.MicroarrayAnnotation (module)
tmtk.annotation.MirnaAnnotation (module)
tmtk.annotation.ProteomicsAnnotation (module)
tmtk.arborist.common (module)
tmtk.arborist.connect_to_baas (module)
tmtk.arborist.jstreecontrol (module)
tmtk.highdim.CopyNumberVariation (module)
tmtk.highdim.Expression (module)
tmtk.highdim.HighDim (module)
tmtk.highdim.HighDimBase (module)
tmtk.highdim.Mirna (module)
tmtk.highdim.Proteomics (module)
tmtk.highdim.ReadCounts (module)
tmtk.highdim.SampleMapping (module)
tmtk.params.AnnotationParams (module)
tmtk.params.ClinicalParams (module)
tmtk.params.HighDimParams (module)
tmtk.params.Params (module)
tmtk.params.ParamsBase (module)
tmtk.params.StudyParams (module)
tmtk.params.TagsParams (module)
tmtk.tags.Tags (module)
tmtk.toolbox.generate_chromosomal_regions_file (module)
tmtk.toolbox.remap_chromosomal_regions (module)
tmtk.toolbox.wizard (module)
tmtk.utils.Exceptions (module)
tmtk.utils.filebase (module)
tmtk.utils.Generic (module)
tmtk.utils.mappings (module)
to_clipboard() (tmtk.arborist.jstreecontrol.JSTree method)
TooManyValues
top_node (tmtk.Study attribute)
trial_visit (tmtk.clinical.Variable attribute)
trial_visits_header (tmtk.utils.mappings.Mappings attribute)
tv_label (tmtk.utils.mappings.Mappings attribute)
tv_unit (tmtk.utils.mappings.Mappings attribute)
tv_value (tmtk.utils.mappings.Mappings attribute)
U
unique_values (tmtk.clinical.Variable attribute)
update_concept_paths() (tmtk.highdim.SampleMapping.SampleMapping method)
update_from_baas() (tmtk.Study method)
update_from_treefile() (tmtk.Study method)
update_high_dim_paths() (tmtk.highdim.HighDim.HighDim method)
update_study_from_json() (in module tmtk.arborist.common)
V
validate_all() (tmtk.annotation.Annotations.Annotations method)
(tmtk.Study method)
(tmtk.clinical.Clinical method)
(tmtk.highdim.HighDim.HighDim method)
values (tmtk.clinical.Variable attribute)
var_id (tmtk.clinical.Variable attribute)
Variable (class in tmtk.clinical)
VIS_CATEGORICAL (tmtk.clinical.Variable attribute)
VIS_DATE (tmtk.clinical.Variable attribute)
VIS_NUMERIC (tmtk.clinical.Variable attribute)
VIS_TEXT (tmtk.clinical.Variable attribute)
visual_attributes (tmtk.clinical.Variable attribute)
W
word_map_changes() (tmtk.clinical.WordMapping method)
word_map_dict (tmtk.clinical.Variable attribute)
word_map_dicts (tmtk.clinical.WordMapping attribute)
word_map_diff() (in module tmtk.utils.Generic)
word_mapped_not_present() (tmtk.clinical.Variable method)
word_mapping (tmtk.arborist.jstreecontrol.ConceptTree attribute)
word_mapping_header (tmtk.utils.mappings.Mappings attribute)
WordMapping (class in tmtk.clinical)
write_to() (tmtk.params.StudyParams.StudyParams method)
(tmtk.Study method)
(tmtk.utils.filebase.FileBase method)
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