Index

A

add() (eco_helper.core.ecotypes.Ecotype method) add_gtf_gene_names() (in module eco_helper.normalise.funcs) add_names() (in module eco_helper.convert.mtx) adopt_name_index() (eco_helper.normalise.NormTable.NormTable method) annotation_columns (eco_helper.core.ecotyper_config.EcoTyperConfig property)

annotation_file (eco_helper.core.ecotyper_config.EcoTyperConfig property) array_to_cpm() (in module eco_helper.normalise.funcs) array_to_tpm() (in module eco_helper.normalise.funcs) assemble_enrichr_results() (in module eco_helper.enrich.funcs) assemble_prerank_results() (in module eco_helper.enrich.funcs) available_formats (in module eco_helper.format.formats)

B

backend (in module eco_helper.enrich.visualise) BaseOverlap (class in eco_helper.core.gene_sets)

bash() (in module eco_helper.core.terminal_funcs) between_tabulars() (in module eco_helper.convert.funcs)

C

call_gtftools() (in module eco_helper.normalise.funcs) cell_type_col (in module eco_helper.core.settings) cell_types (eco_helper.core.ecotypes.Ecotype property) (eco_helper.core.gene_sets.GeneSetCollection property) CellStateCollection (class in eco_helper.core.cell_states) CellTypeCollection (class in eco_helper.core.cell_types)

collect_gene_sets() (in module eco_helper.enrich.funcs) collection_scatterplot() (in module eco_helper.enrich.visualise) compare_gene_overlaps() (eco_helper.core.cell_states.CellStateCollection method) compute_overlap() (eco_helper.core.gene_sets.GeneSetOverlap method) cophentic_cutoff (eco_helper.core.ecotyper_config.EcoTyperConfig property) count_highlights() (eco_helper.enrich.visualise.StateScatterplot method) counts (eco_helper.normalise.NormTable.NormTable property)

D

Dataset (class in eco_helper.core.dataset) dataset (eco_helper.core.ecotyper_config.EcoTyperConfig property) default_metadata (in module eco_helper.convert.seurat)

drop_celltypes() (in module eco_helper.drop.funcs) drop_from_col() (in module eco_helper.drop.funcs) drop_ids() (in module eco_helper.drop.funcs) drop_samples() (in module eco_helper.drop.funcs)

E

eco_helper module eco_helper.convert module eco_helper.convert.funcs module eco_helper.convert.mtx module eco_helper.convert.seurat module eco_helper.convert.tabular module eco_helper.core module eco_helper.core.cell_states module eco_helper.core.cell_types module eco_helper.core.dataset module eco_helper.core.ecotyper_config module eco_helper.core.ecotypes module eco_helper.core.find module eco_helper.core.gene_sets module eco_helper.core.settings module eco_helper.core.terminal_funcs module eco_helper.core.TerminalOutput module eco_helper.drop module eco_helper.drop.funcs module

eco_helper.enrich module eco_helper.enrich.funcs module eco_helper.enrich.visualise module eco_helper.format module eco_helper.format.formats module eco_helper.format.Formatter module eco_helper.format.funcs module eco_helper.format.Pseudo module eco_helper.normalise module eco_helper.normalise.funcs module eco_helper.normalise.NormTable module Ecotype (class in eco_helper.core.ecotypes) ecotype_col (in module eco_helper.core.settings) EcotypeCollection (class in eco_helper.core.ecotypes) EcoTyper (in module eco_helper.format.formats) ecotyper_experiment_col (in module eco_helper.core.settings) EcoTyperConfig (class in eco_helper.core.ecotyper_config) ecotypes_assignment_file (in module eco_helper.core.settings) ecotypes_composition_file (in module eco_helper.core.settings) ecotypes_folder (in module eco_helper.core.settings) enrichr() (in module eco_helper.enrich.funcs) enrichr_ecotypes() (in module eco_helper.enrich.funcs) enrichr_outdir (in module eco_helper.core.settings) enrichr_results_suffix (in module eco_helper.core.settings) export_to_gseapy() (eco_helper.core.cell_states.CellStateCollection method) expression_matrix (eco_helper.core.ecotyper_config.EcoTyperConfig property)

F

filesuffix() (in module eco_helper.convert.funcs) find_files() (in module eco_helper.core.find) find_subdirs() (in module eco_helper.core.find) Formatter (class in eco_helper.format.Formatter)

from_mtx_to_tabular() (in module eco_helper.convert.funcs) from_seurat_to_tabular() (in module eco_helper.convert.funcs) from_tabular_to_mtx() (in module eco_helper.convert.funcs) from_terminal() (in module eco_helper.core.terminal_funcs)

G

gene_col (in module eco_helper.core.settings) gene_info_file (in module eco_helper.core.settings) gene_set_filenames() (eco_helper.core.ecotypes.Ecotype method) gene_sets_outdir (in module eco_helper.core.settings) gene_sets_suffix (in module eco_helper.core.settings) genes (eco_helper.core.ecotypes.Ecotype property) GeneSetCollection (class in eco_helper.core.gene_sets)

GeneSetOverlap (class in eco_helper.core.gene_sets) get() (eco_helper.core.gene_sets.BaseOverlap method) (eco_helper.format.Formatter.Formatter method) (eco_helper.normalise.NormTable.NormTable method) get_genes() (eco_helper.core.cell_states.CellStateCollection method) get_lengths() (eco_helper.normalise.NormTable.NormTable method) gseapy_outdir (in module eco_helper.core.settings)

H

highlight() (eco_helper.enrich.visualise.StateScatterplot method)

I

ids (eco_helper.normalise.NormTable.NormTable property)

index_to_column() (eco_helper.format.Formatter.Formatter method) items() (eco_helper.core.gene_sets.GeneSetCollection method)

K

keys() (eco_helper.core.gene_sets.GeneSetCollection method)

L

lengths (eco_helper.normalise.NormTable.NormTable property)

M

match_genes_to_states() (eco_helper.core.ecotypes.EcotypeCollection method) match_regex_pattern() (in module eco_helper.normalise.funcs) memorize() (eco_helper.normalise.NormTable.NormTable method) module eco_helper eco_helper.convert eco_helper.convert.funcs eco_helper.convert.mtx eco_helper.convert.seurat eco_helper.convert.tabular eco_helper.core eco_helper.core.cell_states eco_helper.core.cell_types eco_helper.core.dataset eco_helper.core.ecotyper_config eco_helper.core.ecotypes eco_helper.core.find eco_helper.core.gene_sets eco_helper.core.settings eco_helper.core.terminal_funcs eco_helper.core.TerminalOutput eco_helper.drop eco_helper.drop.funcs eco_helper.enrich eco_helper.enrich.funcs eco_helper.enrich.visualise eco_helper.format eco_helper.format.formats eco_helper.format.Formatter eco_helper.format.funcs eco_helper.format.Pseudo eco_helper.normalise eco_helper.normalise.funcs eco_helper.normalise.NormTable

N

names (eco_helper.normalise.NormTable.NormTable property)

NormTable (class in eco_helper.normalise.NormTable)

O

output_dir (eco_helper.core.ecotyper_config.EcoTyperConfig property)

P

plot() (eco_helper.enrich.visualise.StateScatterplot method) prerank() (in module eco_helper.enrich.funcs) prerank_ecotypes() (in module eco_helper.enrich.funcs) prerank_outdir (in module eco_helper.core.settings)

prerank_results_suffix (in module eco_helper.core.settings) Pseudo (class in eco_helper.format.Pseudo) PseudoColumns (class in eco_helper.format.Pseudo) PseudoDataFrame (class in eco_helper.format.Pseudo) PseudoIndex (class in eco_helper.format.Pseudo)

R

raw_counts (eco_helper.normalise.NormTable.NormTable property) raw_data (eco_helper.normalise.NormTable.NormTable property) read() (eco_helper.core.dataset.Dataset method) (eco_helper.format.Pseudo.PseudoDataFrame method) (eco_helper.normalise.NormTable.NormTable method) (in module eco_helper.convert.mtx) (in module eco_helper.convert.tabular) read_anotation() (in module eco_helper.core.dataset) read_csv() (in module eco_helper.convert.tabular) read_ecotyper_config() (in module eco_helper.core.ecotyper_config) read_expression() (in module eco_helper.core.dataset) read_formats_file() (in module eco_helper.format.funcs)

read_output() (eco_helper.core.TerminalOutput.TerminalOutput method) read_table() (eco_helper.format.Formatter.Formatter method) read_tsv() (in module eco_helper.convert.tabular) read_txt() (in module eco_helper.convert.tabular) reformat() (eco_helper.format.Formatter.Formatter method) rel_expr_col (in module eco_helper.core.settings) remove() (eco_helper.core.ecotypes.Ecotype method) replace_delims() (eco_helper.format.Pseudo.PseudoDataFrame method) returncode (eco_helper.core.TerminalOutput.TerminalOutput attribute) returncode() (in module eco_helper.core.terminal_funcs) round() (eco_helper.normalise.NormTable.NormTable method) round_values() (in module eco_helper.normalise.funcs) run() (in module eco_helper.core.terminal_funcs)

S

save() (eco_helper.core.cell_states.CellStateCollection method) (eco_helper.core.gene_sets.GeneSetCollection method) (eco_helper.normalise.NormTable.NormTable method) scatterplot() (in module eco_helper.enrich.visualise) separators (in module eco_helper.convert.tabular) set_lengths() (eco_helper.normalise.NormTable.NormTable method) state_assignments_suffix (in module eco_helper.core.settings) state_col (in module eco_helper.core.settings) states (eco_helper.core.ecotypes.Ecotype property)

StateScatterplot (class in eco_helper.enrich.visualise) stderr (eco_helper.core.TerminalOutput.TerminalOutput attribute) stderr() (in module eco_helper.core.terminal_funcs) stdout (eco_helper.core.TerminalOutput.TerminalOutput attribute) stdout() (in module eco_helper.core.terminal_funcs) subsets() (eco_helper.core.gene_sets.GeneSetCollection method) success() (eco_helper.core.TerminalOutput.TerminalOutput method) supported_formats (in module eco_helper.convert.seurat) (in module eco_helper.convert.tabular)

T

TerminalOutput (class in eco_helper.core.TerminalOutput) to_cpm() (eco_helper.normalise.NormTable.NormTable method) to_csv() (eco_helper.format.Pseudo.PseudoDataFrame method) to_df() (eco_helper.core.ecotypes.Ecotype method)

to_dict() (eco_helper.core.ecotypes.Ecotype method) to_tabular() (in module eco_helper.convert.seurat) to_tpm() (eco_helper.normalise.NormTable.NormTable method) top_gene_sets() (eco_helper.enrich.visualise.StateScatterplot method)

V

values() (eco_helper.core.gene_sets.GeneSetCollection method)

W

write() (eco_helper.core.dataset.Dataset method) (in module eco_helper.convert.mtx) (in module eco_helper.convert.tabular) write_annotation() (in module eco_helper.core.dataset)

write_csv() (in module eco_helper.convert.tabular) write_expression() (in module eco_helper.core.dataset) write_table() (eco_helper.format.Formatter.Formatter method) write_tsv() (in module eco_helper.convert.tabular) write_txt() (in module eco_helper.convert.tabular)