kb-python
stable
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API Reference
kb-python
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_
__version__ (in module kb_python)
A
ABUNDANCE_FILENAME (in module kb_python.constants)
ABUNDANCE_GENE_FILENAME (in module kb_python.constants)
ABUNDANCE_GENE_TPM_FILENAME (in module kb_python.constants)
ABUNDANCE_TPM_FILENAME (in module kb_python.constants)
ADATA_PREFIX (in module kb_python.constants)
B
BASIC_TEMPLATE_PATH (in module kb_python.report)
BATCH_FILENAME (in module kb_python.constants)
BINS_DIR (in module kb_python.config)
BUS_CDNA_PREFIX (in module kb_python.constants)
BUS_FILENAME (in module kb_python.constants)
BUS_FILTERED_FILENAME (in module kb_python.constants)
BUS_FILTERED_SUFFIX (in module kb_python.constants)
BUS_INTRON_PREFIX (in module kb_python.constants)
BUS_S_FILENAME (in module kb_python.constants)
BUS_SC_FILENAME (in module kb_python.constants)
BUS_UNFILTERED_FILENAME (in module kb_python.constants)
BUS_UNFILTERED_SUFFIX (in module kb_python.constants)
bustools_capture() (in module kb_python.count)
bustools_correct() (in module kb_python.count)
bustools_count() (in module kb_python.count)
bustools_inspect() (in module kb_python.count)
BUSTOOLS_INSPECT_PARSER (in module kb_python.validate)
BUSTOOLS_PATH (in module kb_python.config)
bustools_project() (in module kb_python.count)
BUSTOOLS_RELEASES_URL (in module kb_python.config)
BUSTOOLS_REPO_URL (in module kb_python.config)
bustools_sort() (in module kb_python.count)
BUSTOOLS_TARBALL_URL (in module kb_python.config)
bustools_whitelist() (in module kb_python.count)
C
CAPTURE_FILENAME (in module kb_python.constants)
CDNA_FILENAME (in module kb_python.constants)
CELLRANGER_BARCODES (in module kb_python.constants)
CELLRANGER_DIR (in module kb_python.constants)
CELLRANGER_GENES (in module kb_python.constants)
CELLRANGER_MATRIX (in module kb_python.constants)
CELLS_FILENAME (in module kb_python.constants)
chemistry (kb_python.config.Technology attribute)
collapse_anndata() (in module kb_python.utils)
COMBINED_FILENAME (in module kb_python.constants)
command() (kb_python.stats.Stats method)
COMMAND_TO_FUNCTION (in module kb_python.main)
compile() (in module kb_python.compile)
compile_bustools() (in module kb_python.compile)
compile_kallisto() (in module kb_python.compile)
COMPILED_DIR (in module kb_python.config)
CompileError
compress_gzip (in module kb_python.utils)
concatenate_files (in module kb_python.utils)
ConfigError
convert_matrices() (in module kb_python.count)
convert_matrix() (in module kb_python.count)
convert_transcripts_to_genes() (in module kb_python.count)
copy_or_create_whitelist() (in module kb_python.count)
copy_whitelist() (in module kb_python.dry.utils)
(in module kb_python.utils)
CORRECT_CODE (in module kb_python.constants)
count() (in module kb_python.count)
count_smartseq3() (in module kb_python.count)
count_velocity() (in module kb_python.count)
count_velocity_smartseq3() (in module kb_python.count)
COUNTS_PREFIX (in module kb_python.constants)
create_10x_feature_barcode_map() (in module kb_python.dry.utils)
(in module kb_python.utils)
create_t2c() (in module kb_python.ref)
create_t2g_from_fasta() (in module kb_python.ref)
D
decompress_file() (in module kb_python.ref)
decompress_gzip (in module kb_python.utils)
description (kb_python.config.Technology attribute)
dict_to_table() (in module kb_python.report)
display_info() (in module kb_python.main)
display_technologies() (in module kb_python.main)
download_file (in module kb_python.utils)
download_reference() (in module kb_python.ref)
DRY (in module kb_python.config)
dryable() (in module kb_python.dry)
dummy_function() (in module kb_python.dry)
E
ECMAP_FILENAME (in module kb_python.constants)
elbow_plot() (in module kb_python.report)
end() (kb_python.stats.Stats method)
execute_report() (in module kb_python.report)
F
FEATURE_NAME (in module kb_python.constants)
FEATURE_PREFIX (in module kb_python.constants)
FILTER_WHITELIST_FILENAME (in module kb_python.constants)
filter_with_bustools() (in module kb_python.count)
FILTERED_CODE (in module kb_python.constants)
FILTERED_COUNTS_DIR (in module kb_python.constants)
find_git_root() (in module kb_python.compile)
FLD_FILENAME (in module kb_python.constants)
FLENS_FILENAME (in module kb_python.constants)
G
GENE_DIR (in module kb_python.constants)
GENE_NAME (in module kb_python.constants)
generate_kite_fasta() (in module kb_python.ref)
genes_detected_plot() (in module kb_python.report)
GENES_FILENAME (in module kb_python.constants)
get_binary_info() (in module kb_python.main)
get_bustools_binary_path() (in module kb_python.config)
get_bustools_url() (in module kb_python.compile)
get_bustools_version() (in module kb_python.utils)
get_compiled_bustools_path() (in module kb_python.config)
get_compiled_kallisto_path() (in module kb_python.config)
get_filename_from_url() (in module kb_python.compile)
get_gtf_attribute_exclude_func() (in module kb_python.ref)
get_gtf_attribute_include_func() (in module kb_python.ref)
get_kallisto_binary_path() (in module kb_python.config)
get_kallisto_url() (in module kb_python.compile)
get_kallisto_version() (in module kb_python.utils)
get_latest_github_release_tag() (in module kb_python.compile)
get_provided_bustools_path() (in module kb_python.config)
get_provided_kallisto_path() (in module kb_python.config)
get_supported_technologies() (in module kb_python.utils)
get_temporary_filename (in module kb_python.utils)
get_temporary_filename() (in module kb_python.dry.utils)
GITHUB_API_URL (in module kb_python.config)
I
import_matrix_as_anndata() (in module kb_python.utils)
import_tcc_matrix_as_anndata() (in module kb_python.utils)
INDEX_FILENAME (in module kb_python.constants)
INFO_FILENAME (in module kb_python.constants)
INSPECT_FILENAME (in module kb_python.constants)
INSPECT_INTERNAL_FILENAME (in module kb_python.constants)
INSPECT_PARSER (in module kb_python.count)
INSPECT_UMI_FILENAME (in module kb_python.constants)
INTERNAL_SUFFIX (in module kb_python.constants)
INTRON_FILENAME (in module kb_python.constants)
is_dry() (in module kb_python.config)
(in module kb_python.dry)
is_validate() (in module kb_python.config)
K
kallisto_bus() (in module kb_python.count)
kallisto_index() (in module kb_python.ref)
KALLISTO_INFO_FILENAME (in module kb_python.constants)
KALLISTO_PATH (in module kb_python.config)
kallisto_quant_tcc() (in module kb_python.count)
KALLISTO_RELEASES_URL (in module kb_python.config)
KALLISTO_REPO_URL (in module kb_python.config)
KALLISTO_TARBALL_URL (in module kb_python.config)
KB_INFO_FILENAME (in module kb_python.constants)
kb_python
module
kb_python.compile
module
kb_python.config
module
kb_python.constants
module
kb_python.count
module
kb_python.dry
module
kb_python.dry.count
module
kb_python.dry.utils
module
kb_python.logging
module
kb_python.main
module
kb_python.ref
module
kb_python.report
module
kb_python.stats
module
kb_python.utils
module
kb_python.validate
module
knee_plot() (in module kb_python.report)
L
logger (in module kb_python.logging)
M
main() (in module kb_python.main)
make_directory() (in module kb_python.dry.utils)
(in module kb_python.utils)
MARGIN (in module kb_python.report)
MATRIX_TEMPLATE_PATH (in module kb_python.report)
matrix_to_cellranger() (in module kb_python.count)
module
kb_python
kb_python.compile
kb_python.config
kb_python.constants
kb_python.count
kb_python.dry
kb_python.dry.count
kb_python.dry.utils
kb_python.logging
kb_python.main
kb_python.ref
kb_python.report
kb_python.stats
kb_python.utils
kb_python.validate
move_file() (in module kb_python.dry.utils)
(in module kb_python.utils)
N
name (kb_python.config.Technology attribute)
no_validate() (in module kb_python.config)
O
open_as_text (in module kb_python.utils)
overlay_anndatas() (in module kb_python.utils)
P
PACKAGE_PATH (in module kb_python.config)
parse_compile() (in module kb_python.main)
parse_count() (in module kb_python.main)
parse_ref() (in module kb_python.main)
parse_technologies() (in module kb_python.utils)
pca_plot() (in module kb_python.report)
PLATFORM (in module kb_python.config)
PROJECT_CODE (in module kb_python.constants)
R
read_t2g() (in module kb_python.utils)
ref() (in module kb_python.ref)
ref_kite() (in module kb_python.ref)
ref_lamanno() (in module kb_python.ref)
Reference (in module kb_python.config)
REFERENCES (in module kb_python.config)
REFERENCES_MAPPING (in module kb_python.config)
RefError
remove_directory() (in module kb_python.dry.utils)
(in module kb_python.utils)
render_report() (in module kb_python.report)
REPORT_DIR (in module kb_python.report)
REPORT_HTML_FILENAME (in module kb_python.constants)
REPORT_NOTEBOOK_FILENAME (in module kb_python.constants)
restore_cwd() (in module kb_python.utils)
run_executable() (in module kb_python.dry.utils)
(in module kb_python.utils)
S
save() (kb_python.stats.Stats method)
SAVED_INDEX_FILENAME (in module kb_python.constants)
set_bustools_binary_path() (in module kb_python.config)
set_dry() (in module kb_python.config)
set_kallisto_binary_path() (in module kb_python.config)
setup_compile_args() (in module kb_python.main)
setup_count_args() (in module kb_python.main)
setup_info_args() (in module kb_python.main)
setup_ref_args() (in module kb_python.main)
show (kb_python.config.Technology attribute)
SORT_CODE (in module kb_python.constants)
SORTED_FASTA_FILENAME (in module kb_python.constants)
SORTED_GTF_FILENAME (in module kb_python.constants)
split_and_index() (in module kb_python.ref)
start() (kb_python.stats.Stats method)
Stats (class in kb_python.stats)
STATS (in module kb_python.stats)
stream_batch() (in module kb_python.count)
(in module kb_python.dry.count)
stream_fastqs() (in module kb_python.count)
stream_file() (in module kb_python.dry.utils)
(in module kb_python.utils)
sum_anndatas() (in module kb_python.utils)
T
TCC_PREFIX (in module kb_python.constants)
TECHNOLOGIES (in module kb_python.config)
TECHNOLOGIES_MAPPING (in module kb_python.config)
Technology (class in kb_python.config)
TECHNOLOGY_PARSER (in module kb_python.utils)
TEMP_DIR (in module kb_python.config)
test_binaries() (in module kb_python.main)
to_dict() (kb_python.stats.Stats method)
TRANSCRIPT_NAME (in module kb_python.constants)
TXNAMES_FILENAME (in module kb_python.constants)
U
UMI_SUFFIX (in module kb_python.constants)
undryable_function() (in module kb_python.dry)
UNFILTERED_CODE (in module kb_python.constants)
UNFILTERED_COUNTS_DIR (in module kb_python.constants)
UNFILTERED_QUANT_DIR (in module kb_python.constants)
UnsupportedOSError
update_filename() (in module kb_python.utils)
V
VALIDATE (in module kb_python.config)
validate() (in module kb_python.validate)
validate_bus() (in module kb_python.validate)
validate_files() (in module kb_python.validate)
validate_mtx() (in module kb_python.validate)
ValidateError
VALIDATORS (in module kb_python.validate)
VERSION_PARSER (in module kb_python.utils)
W
WHITELIST_FILENAME (in module kb_python.constants)
whitelist_provided() (in module kb_python.utils)
write_report() (in module kb_python.report)
write_smartseq3_capture() (in module kb_python.count)
(in module kb_python.dry.count)
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