Index

A

add_mapped_column() (in module danrerlib.mapping)

add_mapped_ortholog_column() (in module danrerlib.mapping)

B

bar_chart() (in module danrerlib.enrichplots) build_gene_mapping() (in module danrerlib.mapping)

build_gene_ontology_database() (in module danrerlib.GO) build_kegg_database() (in module danrerlib.KEGG) build_ortho_mapping() (in module danrerlib.mapping)

C

check_valid_human_gene_id_type() (in module danrerlib.utils) check_valid_organism() (in module danrerlib.utils) check_valid_zebrafish_gene_id_type() (in module danrerlib.utils)

convert_ids() (in module danrerlib.mapping) convert_to_human() (in module danrerlib.mapping) convert_to_zebrafish() (in module danrerlib.mapping)

D

danrerlib module danrerlib.database module danrerlib.enrichment module danrerlib.enrichplots module danrerlib.GO module danrerlib.KEGG module

danrerlib.mapping module danrerlib.settings module danrerlib.utils module DATABASE_DIR (in module danrerlib.settings) DatabaseNotFoundError dotplot() (in module danrerlib.enrichplots) download_url() (in module danrerlib.utils) download_url_to_file() (in module danrerlib.utils)

E

enrich_fishers() (in module danrerlib.enrichment)

enrich_logistic() (in module danrerlib.enrichment) ENS_ID (in module danrerlib.settings)

F

FILE_DIR (in module danrerlib.settings)

G

get_genes_in_disease() (in module danrerlib.KEGG) get_genes_in_GO_concept() (in module danrerlib.GO) get_genes_in_pathway() (in module danrerlib.KEGG)

get_ortho_ids() (in module danrerlib.mapping) get_text_positions() (in module danrerlib.enrichplots) GO_DATA_DIR (in module danrerlib.settings)

H

HUMAN_ID (in module danrerlib.settings)

I

id_exists_given_organism() (in module danrerlib.GO)

InvalidGeneTypeError, [1] InvalidOrganismError

K

kegg_background_gene_set (in module danrerlib.KEGG)

KEGG_DATA_DIR (in module danrerlib.settings)

L

load_data() (in module danrerlib.utils)

M

MASTER_MAPPING_FILE_PATH (in module danrerlib.settings) MASTER_ORTHO_FILE_PATH (in module danrerlib.settings) module danrerlib danrerlib.database danrerlib.enrichment danrerlib.enrichplots danrerlib.GO danrerlib.KEGG danrerlib.mapping danrerlib.settings danrerlib.utils

N

NCBI_ID (in module danrerlib.settings)

normalize_gene_id_type() (in module danrerlib.utils) normalize_organism_name() (in module danrerlib.utils)

P

pretty_print_series() (in module danrerlib.utils)

R

RAW_DATA_DIR (in module danrerlib.settings)

S

save_data() (in module danrerlib.utils)

SYMBOL (in module danrerlib.settings)

T

text_plotter() (in module danrerlib.enrichplots)

V

VERSION_NUM (in module danrerlib.settings)

volcano() (in module danrerlib.enrichplots)

Z

ZFIN_ID (in module danrerlib.settings)