tmtk
0.3.2
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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_metadata() (tmtk.Study 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)
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_column_mapping_template() (tmtk.clinical.Clinical method)
B
biomarkers (tmtk.annotation.ChromosomalRegions.ChromosomalRegions attribute)
(tmtk.annotation.MicroarrayAnnotation.MicroarrayAnnotation attribute)
(tmtk.annotation.MirnaAnnotation.MirnaAnnotation attribute)
(tmtk.annotation.ProteomicsAnnotation.ProteomicsAnnotation attribute)
build_index() (tmtk.clinical.ColumnMapping method)
(tmtk.clinical.WordMapping method)
C
call_boris() (in module tmtk.arborist.common)
(tmtk.Study method)
(tmtk.clinical.Clinical method)
cat_cd (tmtk.utils.mappings.Mappings attribute)
cat_cd_s (tmtk.utils.mappings.Mappings 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)
ColumnMapping (class in tmtk.clinical)
(tmtk.clinical.Clinical 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
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)
find_annotation() (tmtk.Study method)
find_fully_unique_columns() (in module tmtk.utils.Generic)
find_params_for_datatype() (tmtk.Study 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() (tmtk.params.ParamsBase.ParamsBase method)
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_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_with_prop() (tmtk.Study method)
get_params() (tmtk.utils.mappings.Mappings static method)
get_tags() (tmtk.tags.Tags.MetaDataTags method)
get_variable() (tmtk.clinical.Clinical method)
get_word_map() (tmtk.clinical.WordMapping method)
H
header (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)
invalid_paths (tmtk.tags.Tags.MetaDataTags attribute)
is_empty (tmtk.clinical.Variable attribute)
is_in_wordmap (tmtk.clinical.Variable attribute)
is_numeric (tmtk.clinical.Variable attribute)
is_numeric() (in module tmtk.utils.Generic)
is_numeric_in_datafile (tmtk.clinical.Variable attribute)
is_viable() (tmtk.params.AnnotationParams.AnnotationParams method)
(tmtk.params.ClinicalParams.ClinicalParams method)
(tmtk.params.HighDimParams.HighDimParams method)
(tmtk.params.StudyParams.StudyParams 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 (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)
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)
Mirna (class in tmtk.highdim.Mirna)
MirnaAnnotation (class in tmtk.annotation.MirnaAnnotation)
MyEncoder (class in tmtk.arborist.jstreecontrol)
N
name (tmtk.utils.filebase.FileBase attribute)
NotYetImplemented
numeric() (in module tmtk.utils.Generic)
O
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)
ParamsBase (class in tmtk.params.ParamsBase)
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)
remap_chromosomal_regions() (in module tmtk.toolbox.remap_chromosomal_regions)
remap_to() (tmtk.highdim.CopyNumberVariation.CopyNumberVariation method)
(tmtk.highdim.ReadCounts.ReadCounts method)
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.params.ParamsBase.ParamsBase method)
(tmtk.utils.filebase.FileBase method)
select_row() (tmtk.clinical.ColumnMapping method)
set_concept_path() (tmtk.clinical.ColumnMapping method)
show_changes() (tmtk.clinical.Clinical method)
slice_path() (tmtk.highdim.SampleMapping.SampleMapping method)
start_session() (in module tmtk.arborist.connect_to_baas)
Study (class in tmtk)
study_id (tmtk.highdim.SampleMapping.SampleMapping attribute)
(tmtk.Study attribute)
study_name (tmtk.Study attribute)
StudyParams (class in tmtk.params.StudyParams)
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)
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
U
unique_values (tmtk.clinical.Variable attribute)
update() (tmtk.params.ParamsBase.ParamsBase method)
update_clinical_from_json() (in module tmtk.arborist.common)
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
valid_arborist_or_exception() (in module tmtk.arborist.common)
validate() (tmtk.clinical.Variable method)
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)
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_mapping (tmtk.arborist.jstreecontrol.ConceptTree attribute)
word_mapping_header (tmtk.utils.mappings.Mappings attribute)
WordMapping (class in tmtk.clinical)
(tmtk.clinical.Clinical attribute)
write_to() (tmtk.params.ParamsBase.ParamsBase method)
(tmtk.Study method)
(tmtk.utils.filebase.FileBase method)
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