Index

Symbols

--binsize linkapy-CLI-parsing command line option --blacklist linkapy-CLI-parsing command line option --chromsizes linkapy-CLI-parsing command line option --help linkapy-CLI command line option linkapy-CLI-example command line option linkapy-CLI-parsing command line option --methylation_path linkapy-CLI-parsing command line option --methylation_pattern linkapy-CLI-parsing command line option --methylation_pattern_names linkapy-CLI-parsing command line option --NOMe linkapy-CLI-parsing command line option --output linkapy-CLI-example command line option linkapy-CLI-parsing command line option --project linkapy-CLI-parsing command line option --regions linkapy-CLI-parsing command line option --threads linkapy-CLI-parsing command line option --transcriptome_path linkapy-CLI-parsing command line option --transcriptome_pattern linkapy-CLI-parsing command line option

--transcriptome_pattern_names linkapy-CLI-parsing command line option --verbose linkapy-CLI-parsing command line option --version linkapy-CLI command line option -b linkapy-CLI-parsing command line option -c linkapy-CLI-parsing command line option -h linkapy-CLI command line option linkapy-CLI-example command line option linkapy-CLI-parsing command line option -j linkapy-CLI-parsing command line option -m linkapy-CLI-parsing command line option -o linkapy-CLI-example command line option linkapy-CLI-parsing command line option -p linkapy-CLI-parsing command line option -r linkapy-CLI-parsing command line option -t linkapy-CLI-parsing command line option -v linkapy-CLI-parsing command line option

_

_download_and_verify() (linkapy.example.Linkapy_Example method)

_glob() (linkapy.parsing.Linkapy_Parser method) _validate() (linkapy.parsing.Linkapy_Parser method)

B

binsize (linkapy.parsing.Linkapy_Parser attribute)

blacklist (linkapy.parsing.Linkapy_Parser attribute)

C

chromsizes (linkapy.parsing.Linkapy_Parser attribute)

D

dump_mudata() (linkapy.parsing.Linkapy_Parser method)

G

get_common_cellname() (in module linkapy.parsing)

L

linkapy module linkapy-CLI command line option --help --version -h linkapy-CLI-example command line option --help --output -h -o linkapy-CLI-parsing command line option --binsize --blacklist --chromsizes --help --methylation_path --methylation_pattern --methylation_pattern_names --NOMe --output --project --regions --threads --transcriptome_path --transcriptome_pattern --transcriptome_pattern_names --verbose -b -c -h -j -m -o -p -r -t -v

linkapy.example module linkapy.logger module linkapy.parsing module Linkapy_Example (class in linkapy.example) Linkapy_Parser (class in linkapy.parsing) logfile (linkapy.example.Linkapy_Example attribute) (linkapy.parsing.Linkapy_Parser attribute) logger (linkapy.example.Linkapy_Example attribute) (linkapy.parsing.Linkapy_Parser attribute)

M

match_cells() (in module linkapy.parsing) md5 (linkapy.example.Linkapy_Example attribute) methylation_path (linkapy.parsing.Linkapy_Parser attribute) methylation_pattern (linkapy.parsing.Linkapy_Parser attribute) methylation_pattern_names (linkapy.parsing.Linkapy_Parser attribute)

module linkapy linkapy.example linkapy.logger linkapy.parsing

O

output (linkapy.example.Linkapy_Example attribute) (linkapy.parsing.Linkapy_Parser attribute)

P

parse() (linkapy.parsing.Linkapy_Parser method)

parse_rna() (in module linkapy.parsing) project (linkapy.parsing.Linkapy_Parser attribute)

R

read_meth_to_anndata() (in module linkapy.parsing)

read_rna_to_anndata() (in module linkapy.parsing) regions (linkapy.parsing.Linkapy_Parser attribute)

S

setup_logger() (in module linkapy.logger)

T

threads (linkapy.parsing.Linkapy_Parser attribute) transcriptome_path (linkapy.parsing.Linkapy_Parser attribute)

transcriptome_pattern (linkapy.parsing.Linkapy_Parser attribute) transcriptome_pattern_names (linkapy.parsing.Linkapy_Parser attribute)

U

url (linkapy.example.Linkapy_Example attribute)