Orange3 Bioinformatics
stable
Orange3-Bioinformatics
Widgets
Scripting Reference
Orange3 Bioinformatics
Index
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Index
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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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F
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G
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H
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I
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K
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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
_
__contains__() (Ontology method)
__getitem__() (Ontology method)
__init__() (GDSInfo method)
(Gene method)
(GeneInfo method)
(GeneMatcher method)
__iter__() (Ontology method)
__len__() (Ontology method)
A
aaseq (GeneEntry property)
add() (Annotations method)
add_annotation() (Annotations method)
all_reac (EnzymeEntry property)
annotate_projection() (in module orangecontrib.bioinformatics.annotation.annotate_projection)
annotate_samples() (AnnotateSamples static method)
AnnotateSamples (class in orangecontrib.bioinformatics.annotation.annotate_samples)
annotation (GenomeEntry property)
AnnotationRecord (class in orangecontrib.bioinformatics.go)
annotations (Annotations attribute)
Annotations (class in orangecontrib.bioinformatics.go)
append() (Annotations method)
assign_annotations() (AnnotateSamples static method)
assign_labels() (in module orangecontrib.bioinformatics.annotation.annotate_projection)
atom (CompoundEntry property)
B
batch_get() (DBDataBase method)
bond (CompoundEntry property)
brite (CompoundEntry property)
(GeneEntry property)
C
chromosome (GenomeEntry property)
class_ (EnzymeEntry property)
(GeneEntry property)
(PathwayEntry property)
cluster_additional_points() (in module orangecontrib.bioinformatics.annotation.annotate_projection)
cluster_data() (in module orangecontrib.bioinformatics.annotation.annotate_projection)
comment (CompoundEntry property)
(EnzymeEntry property)
(GenomeEntry property)
common_hierarchy() (GeneSets method)
common_org() (GeneSets method)
common_taxid_to_name() (in module orangecontrib.bioinformatics.ncbi.taxonomy)
common_taxids() (in module orangecontrib.bioinformatics.ncbi.taxonomy)
Compound (class in orangecontrib.bioinformatics.kegg.databases)
compound (PathwayEntry property)
CompoundEntry (class in orangecontrib.bioinformatics.kegg.databases)
compute_concave_hulls() (in module orangecontrib.bioinformatics.annotation.annotate_projection)
connect() (in module orangecontrib.bioinformatics.resolwe)
D
D. dictyostelium
mutants
data_source (GenomeEntry property)
DB (Compound attribute)
(DBDataBase attribute)
(Enzyme attribute)
(Genes attribute)
(Genome attribute)
(Pathway attribute)
(Reaction attribute)
DBDataBase (class in orangecontrib.bioinformatics.kegg.databases)
DBEntry (class in orangecontrib.bioinformatics.kegg.entry)
DBGETEntryParser (class in orangecontrib.bioinformatics.kegg.entry.parser)
dblinks (CompoundEntry property)
(EnzymeEntry property)
(GeneEntry property)
(PathwayEntry property)
def_ (Term attribute)
defined_slims_subsets() (Ontology method)
definition (GeneEntry property)
(GenomeEntry property)
(ReactionEntry property)
description (PathwayEntry property)
disease (GeneEntry property)
(GenomeEntry property)
(PathwayEntry property)
download_etc_data() (GenAPI method)
drug (PathwayEntry property)
drug_target (GeneEntry property)
E
edges_to_polygon() (in module orangecontrib.bioinformatics.annotation.annotate_projection)
entry (CompoundEntry property)
(EnzymeEntry property)
(GeneEntry property)
(GenomeEntry property)
(PathwayEntry property)
(ReactionEntry property)
ENTRY_END (DBGETEntryParser attribute)
entry_key (DBEntry property)
ENTRY_START (DBGETEntryParser attribute)
ENTRY_TYPE (Compound attribute)
(DBDataBase attribute)
(Enzyme attribute)
(Genes attribute)
(Genome attribute)
(Pathway attribute)
(Reaction attribute)
Enzyme (class in orangecontrib.bioinformatics.kegg.databases)
enzyme (CompoundEntry property)
(PathwayEntry property)
(ReactionEntry property)
EnzymeEntry (class in orangecontrib.bioinformatics.kegg.databases)
equation (ReactionEntry property)
exact_mass (CompoundEntry property)
extend() (Annotations method)
extract_sub_graph() (Ontology method)
extract_super_graph() (Ontology method)
F
fetch_etc_objects() (GenAPI method)
filename() (in module orangecontrib.bioinformatics.geneset)
filename_parse() (in module orangecontrib.bioinformatics.geneset)
filter_annotations() (AnnotateSamples static method)
find() (DBDataBase method)
format() (DBEntry method)
formula (CompoundEntry property)
from_gmt_file_format() (GeneSets static method)
from_string() (AnnotationRecord class method)
from_taxid() (in module orangecontrib.bioinformatics.kegg)
G
GDS (in module orangecontrib.bioinformatics.geo.dataset)
GDSInfo (class in orangecontrib.bioinformatics.geo.dataset)
GenAPI (class in orangecontrib.bioinformatics.resolwe)
Gene (class in orangecontrib.bioinformatics.ncbi.gene)
Gene Expression Omnibus
gene info
gene name matching
gene set
gene sets
gene_aliases() (Organism method)
gene_annotations (Annotations attribute)
gene_mutants() (in module orangecontrib.bioinformatics.dicty.phenotypes)
GeneEntry (class in orangecontrib.bioinformatics.kegg.databases)
GeneInfo (class in orangecontrib.bioinformatics.ncbi.gene)
GeneMatcher (class in orangecontrib.bioinformatics.ncbi.gene)
Genes (class in orangecontrib.bioinformatics.kegg.databases)
genes (EnzymeEntry property)
(Organism property)
genes() (GeneSets method)
(in module orangecontrib.bioinformatics.dicty.phenotypes)
GeneSet (class in orangecontrib.bioinformatics.geneset)
GeneSets (class in orangecontrib.bioinformatics.geneset)
Genome (class in orangecontrib.bioinformatics.kegg.databases)
GenomeEntry (class in orangecontrib.bioinformatics.kegg.databases)
GEO
get() (DBDataBase method)
get_annotated_terms() (Annotations method)
get_annotations_by_go_id() (Annotations method)
get_enriched_pathways() (Organism method)
get_enriched_terms() (Annotations method)
get_entry() (DBDataBase method)
get_epsilon() (in module orangecontrib.bioinformatics.annotation.annotate_projection)
get_genes_by_go_term() (Annotations method)
get_genes_with_known_annotation() (Annotations method)
get_image() (Pathway method)
get_known_genes() (GeneMatcher method)
get_pathways_by_genes() (Organism method)
get_text() (DBDataBase method)
gmt_description() (GeneSet method)
H
hierarchies() (GeneSets method)
homolog_gene() (Gene method)
I
id (Term attribute)
image (Pathway property)
is_a (Term attribute)
items() (DBDataBase method)
iteritems() (DBDataBase method)
iterkeys() (DBDataBase method)
itervalues() (DBDataBase method)
K
KEGGOrganism (in module orangecontrib.bioinformatics.kegg)
keys() (DBDataBase method)
keywords (GenomeEntry property)
ko_pathway (PathwayEntry property)
L
labels_locations() (in module orangecontrib.bioinformatics.annotation.annotate_projection)
lineage() (in module orangecontrib.bioinformatics.ncbi.taxonomy)
link (Pathway property)
list() (Pathway class method)
list_all() (in module orangecontrib.bioinformatics.geneset)
list_pathways() (Organism method)
load_gene_sets() (in module orangecontrib.bioinformatics.geneset)
log_cpm() (AnnotateSamples static method)
M
mann_whitney_test() (AnnotateSamples static method)
match_table_attributes() (GeneMatcher method)
match_table_column() (GeneMatcher method)
microarray data sets
module
orangecontrib.bioinformatics.annotation.annotate_projection
orangecontrib.bioinformatics.dicty.phenotypes
orangecontrib.bioinformatics.geneset
orangecontrib.bioinformatics.go
orangecontrib.bioinformatics.kegg
orangecontrib.bioinformatics.resolwe
module (GeneEntry property)
(PathwayEntry property)
mol_weight (CompoundEntry property)
motif (GeneEntry property)
mutant phenotypes
mutant_genes() (in module orangecontrib.bioinformatics.dicty.phenotypes)
mutant_phenotypes() (in module orangecontrib.bioinformatics.dicty.phenotypes)
mutants() (in module orangecontrib.bioinformatics.dicty.phenotypes)
N
name (CompoundEntry property)
(EnzymeEntry property)
(GeneEntry property)
(GenomeEntry property)
(Pathway property)
(PathwayEntry property)
(ReactionEntry property)
name() (in module orangecontrib.bioinformatics.ncbi.taxonomy)
named_slims_subset() (Ontology method)
namespace (Term attribute)
NCBI
,
[1]
ntseq (GeneEntry property)
number (Pathway property)
O
Ontology (class in orangecontrib.bioinformatics.go)
orangecontrib.bioinformatics.annotation.annotate_projection
module
orangecontrib.bioinformatics.dicty.phenotypes
module
orangecontrib.bioinformatics.geneset
module
orangecontrib.bioinformatics.go
module
orangecontrib.bioinformatics.kegg
module
orangecontrib.bioinformatics.resolwe
module
org (Organism property)
(Pathway property)
org_code (GenomeEntry property)
org_code_to_entry_key() (Genome method)
Organism (class in orangecontrib.bioinformatics.kegg)
organism (GeneEntry property)
(PathwayEntry property)
organism_code (GenomeEntry property)
organism_name_search() (in module orangecontrib.bioinformatics.kegg)
original_db (GenomeEntry property)
orthology (EnzymeEntry property)
(GeneEntry property)
other_names() (in module orangecontrib.bioinformatics.ncbi.taxonomy)
P
parse() (DBEntry method)
Pathway (class in orangecontrib.bioinformatics.kegg.databases)
(class in orangecontrib.bioinformatics.kegg.pathway)
pathway (CompoundEntry property)
(EnzymeEntry property)
(GeneEntry property)
pathway_map (PathwayEntry property)
PathwayEntry (class in orangecontrib.bioinformatics.kegg.databases)
pathways() (in module orangecontrib.bioinformatics.kegg)
(Organism method)
phenotype_mutants() (in module orangecontrib.bioinformatics.dicty.phenotypes)
phenotypes
phenotypes() (in module orangecontrib.bioinformatics.dicty.phenotypes)
plasmid (GenomeEntry property)
position (GeneEntry property)
pre_cache() (DBDataBase method)
product (EnzymeEntry property)
R
Reaction (class in orangecontrib.bioinformatics.kegg.databases)
reaction (CompoundEntry property)
(EnzymeEntry property)
ReactionEntry (class in orangecontrib.bioinformatics.kegg.databases)
reference (CompoundEntry property)
(EnzymeEntry property)
(GenomeEntry property)
(PathwayEntry property)
rel_pathway (PathwayEntry property)
related (Term attribute)
remark (CompoundEntry property)
S
search() (Genome method)
(in module orangecontrib.bioinformatics.ncbi.taxonomy)
SECTION_END (DBGETEntryParser attribute)
SECTION_START (DBGETEntryParser attribute)
set_enrichment() (GeneSet method)
set_slims_subset() (Ontology method)
slims_for_term() (Ontology method)
split_by_hierarchy() (GeneSets method)
statistics (GenomeEntry property)
structure (GeneEntry property)
SUBSECTION_END (DBGETEntryParser attribute)
SUBSECTION_START (DBGETEntryParser attribute)
substrate (EnzymeEntry property)
sysname (EnzymeEntry property)
T
taxid (GenomeEntry property)
taxonomy (GenomeEntry property)
Term (class in orangecontrib.bioinformatics.go)
term_anotations (Annotations attribute)
TEXT (DBGETEntryParser attribute)
title (Pathway property)
to_data_table() (GeneMatcher method)
to_gmt_file_format() (GeneSets method)
to_taxid() (in module orangecontrib.bioinformatics.kegg)
U
update() (GeneSets method)
V
values() (DBDataBase method)
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