Index

_

_RESOURCE_TYPE (recount3._descriptions.R3ResourceDescription attribute)

_TYPE_REGISTRY (recount3._descriptions.R3ResourceDescription attribute)

A

add() (recount3.bundle.R3ResourceBundle method) annotation_ext() (in module recount3.search) annotation_options() (in module recount3.search)

arcname (recount3.resource.R3Resource property) available_projects() (in module recount3.search) available_samples() (in module recount3.search)

B

base_url (recount3.config.Config attribute) BigWigFile (class in recount3._bigwig)

bigwigs() (recount3.bundle.R3ResourceBundle method) build_ranged_summarized_experiment() (in module recount3.se) build_summarized_experiment() (in module recount3.se)

C

cache_dir (recount3.config.Config attribute) cache_disabled (recount3.config.Config attribute) CacheMode (in module recount3.types) chroms() (recount3._bigwig.BigWigFile method) chunk_size (recount3.config.Config attribute) clear_loaded() (recount3.resource.R3Resource method) close() (recount3._bigwig.BigWigFile method) CompatibilityError CompatibilityMode (in module recount3.types)

compute_read_counts() (in module recount3.se) compute_scale_factors() (in module recount3.se) compute_tpm() (in module recount3.se) Config (class in recount3.config) config (recount3.resource.R3Resource attribute) ConfigurationError counts() (recount3.bundle.R3ResourceBundle method) create_ranged_summarized_experiment() (in module recount3.se) create_rse() (in module recount3.se) create_sample_project_lists() (in module recount3.search)

D

data_source (recount3.bundle.R3ResourceBundle attribute) default_config() (in module recount3.config) description (recount3.resource.R3Resource attribute)

discover() (recount3.bundle.R3ResourceBundle class method) download() (recount3.bundle.R3ResourceBundle method) (recount3.resource.R3Resource method) DownloadError

E

exclude_metadata() (recount3.bundle.R3ResourceBundle method)

expand_sra_attributes() (in module recount3.se) extend() (recount3.bundle.R3ResourceBundle method)

F

FieldSpec (in module recount3.types)

filepath (recount3.resource.R3Resource attribute) filter() (recount3.bundle.R3ResourceBundle method)

G

get_loaded() (recount3.bundle.R3ResourceBundle method) (recount3.resource.R3Resource method)

H

header() (recount3._bigwig.BigWigFile method)

I

insecure_ssl (recount3.config.Config attribute) intervals() (recount3._bigwig.BigWigFile method) is_loaded() (recount3.resource.R3Resource method)

is_open() (recount3._bigwig.BigWigFile method) is_paired_end() (in module recount3.se) iter_bigwig() (recount3.bundle.R3ResourceBundle method) iter_loaded() (recount3.bundle.R3ResourceBundle method)

L

load() (recount3.bundle.R3ResourceBundle method) (recount3.resource.R3Resource method)

LoadError

M

match_spec() (in module recount3.search) max_retries (recount3.config.Config attribute) metadata() (recount3.bundle.R3ResourceBundle method) mode (recount3._bigwig.BigWigFile attribute) module recount3 recount3._bigwig recount3._descriptions recount3.bundle recount3.config recount3.errors recount3.resource recount3.se recount3.search recount3.types

O

only_counts() (recount3.bundle.R3ResourceBundle method)

only_metadata() (recount3.bundle.R3ResourceBundle method) organism (recount3.bundle.R3ResourceBundle attribute)

P

path (recount3._bigwig.BigWigFile attribute)

project (recount3.bundle.R3ResourceBundle attribute) project_homes() (in module recount3.search)

R

R3Annotations (class in recount3._descriptions) R3BigWig (class in recount3._descriptions) R3DataSourceMetadata (class in recount3._descriptions) R3DataSources (class in recount3._descriptions) R3GeneOrExonCounts (class in recount3._descriptions) R3JunctionCounts (class in recount3._descriptions) R3ProjectMetadata (class in recount3._descriptions) R3Resource (class in recount3.resource) R3ResourceBundle (class in recount3.bundle) R3ResourceDescription (class in recount3._descriptions) recount3 module recount3._bigwig module recount3._descriptions module recount3.bundle module

recount3.config module recount3.errors module recount3.resource module recount3.se module recount3.search module recount3.types module recount3_cache() (in module recount3.config) recount3_cache_files() (in module recount3.config) recount3_cache_rm() (in module recount3.config) Recount3Error register_type() (recount3._descriptions.R3ResourceDescription class method) resource_type (recount3._descriptions.R3ResourceDescription attribute) resources (recount3.bundle.R3ResourceBundle attribute)

S

samples() (recount3.bundle.R3ResourceBundle method) samples_for_project() (in module recount3.search) search_annotations() (in module recount3.search) search_bigwig_files() (in module recount3.search) search_count_files_gene_or_exon() (in module recount3.search) search_count_files_junctions() (in module recount3.search)

search_data_source_metadata() (in module recount3.search) search_data_sources() (in module recount3.search) search_metadata_files() (in module recount3.search) search_project_all() (in module recount3.search) stack_count_matrices() (recount3.bundle.R3ResourceBundle method) stats() (recount3._bigwig.BigWigFile method) StringOrIterable (in module recount3.types)

T

timeout (recount3.config.Config attribute) to_ranged_summarized_experiment() (recount3.bundle.R3ResourceBundle method)

to_summarized_experiment() (recount3.bundle.R3ResourceBundle method) transform_counts() (in module recount3.se)

U

url (recount3.resource.R3Resource attribute) url_path() (recount3._descriptions.R3Annotations method) (recount3._descriptions.R3BigWig method) (recount3._descriptions.R3DataSourceMetadata method) (recount3._descriptions.R3DataSources method) (recount3._descriptions.R3GeneOrExonCounts method) (recount3._descriptions.R3JunctionCounts method) (recount3._descriptions.R3ProjectMetadata method) (recount3._descriptions.R3ResourceDescription method)

user_agent (recount3.config.Config attribute)

V

values() (recount3._bigwig.BigWigFile method)

W

where() (recount3.bundle.R3ResourceBundle method)