Index

C

comparison_dim_reduction() (in module dim_reduction)

create_dict() (in module extract_gene_ids2name)

D

dim_reduction module

E

extract_gene_ids2name module

F

feature_reduction() (in module machine_learning_tool) fileUtils.file_handling module

fileUtils.metadata_handling module

G

get_attribute() (in module get_protein_atlas) get_files() (in module fileUtils.file_handling) get_files_and_sample_ids() (in module fileUtils.file_handling)

get_protein_atlas module grid_search() (in module machine_learning_tool)

I

icgc_metadata_processing module

L

lines() (in module extract_gene_ids2name)

M

machine_learning_tool module max_features_arr() (in module machine_learning_tool) merge_frames() (in module merge_gene_counts) merge_gene_counts module merge_replica module merge_replica() (in module merge_replica) metadata_processing module module dim_reduction extract_gene_ids2name fileUtils.file_handling fileUtils.metadata_handling get_protein_atlas icgc_metadata_processing machine_learning_tool merge_gene_counts merge_replica metadata_processing parseFeatureCounts parseTPM sra_metadata_processing tcga_metadata_processing xml_soup

P

parse() (in module extract_gene_ids2name) parse_all_fields_csv() (in module sra_metadata_processing) parse_csv() (in module fileUtils.file_handling) parse_featureCounts() (in module parseFeatureCounts) parse_icgc_json_files() (in module icgc_metadata_processing) (in module metadata_processing) parse_soup() (in module xml_soup) parse_stringTie() (in module parseTPM) parse_tcga_json_files() (in module metadata_processing) (in module tcga_metadata_processing)

parse_xml() (in module sra_metadata_processing) parseFeatureCounts module parseTPM module plot_bar() (in module machine_learning_tool) plotly_comparison() (in module dim_reduction) print_mean_std_scores() (in module machine_learning_tool)

R

read_dataset() (in module machine_learning_tool) read_metadata() (in module dim_reduction) (in module fileUtils.metadata_handling) (in module merge_replica)

read_tpm() (in module fileUtils.file_handling) read_unique_genes() (in module fileUtils.file_handling)

S

scaling() (in module dim_reduction) search_space() (in module machine_learning_tool)

silhouette_plot() (in module dim_reduction) sra_metadata_processing module

T

tcga_metadata_processing module

V

visualization_plots() (in module dim_reduction)

W

write_genes() (in module extract_gene_ids2name) write_icgc_table() (in module icgc_metadata_processing) write_lengths() (in module parseFeatureCounts)

write_table() (in module fileUtils.file_handling) write_tcga_table() (in module tcga_metadata_processing) write_xml_table() (in module sra_metadata_processing)

X

xml_soup module