kb-python
v0.24.4
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API Reference
kb-python
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__version__ (in module kb_python)
A
ADATA_PREFIX (in module kb_python.constants)
B
BASEPAIRS (kb_python.fasta.FASTA attribute)
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_sort() (in module kb_python.count)
bustools_whitelist() (in module kb_python.count)
C
CDNA_FILENAME (in module kb_python.constants)
COMBINED_FILENAME (in module kb_python.constants)
COMMAND_TO_FUNCTION (in module kb_python.main)
compress_gzip() (in module kb_python.utils)
concatenate_files() (in module kb_python.utils)
convert_matrix_to_h5ad() (in module kb_python.count)
convert_matrix_to_loom() (in module kb_python.count)
copy_or_create_whitelist() (in module kb_python.count)
copy_whitelist() (in module kb_python.utils)
count() (in module kb_python.count)
count_velocity() (in module kb_python.count)
COUNTS_PREFIX (in module kb_python.constants)
create_t2c() (in module kb_python.ref)
create_t2g_from_fasta() (in module kb_python.ref)
create_t2g_from_gtf() (in module kb_python.ref)
D
decompress_file() (in module kb_python.ref)
decompress_gzip() (in module kb_python.utils)
display_info() (in module kb_python.main)
display_technologies() (in module kb_python.main)
download_reference() (in module kb_python.ref)
E
ECMAP_FILENAME (in module kb_python.constants)
entries() (kb_python.fasta.FASTA method)
(kb_python.gtf.GTF method)
F
FASTA (class in kb_python.fasta)
FILTER_WHITELIST_FILENAME (in module kb_python.constants)
filter_with_bustools() (in module kb_python.count)
FILTERED_COUNTS_DIR (in module kb_python.constants)
G
generate_cdna_fasta() (in module kb_python.fasta)
generate_intron_fasta() (in module kb_python.fasta)
generate_spliced_fasta() (in module kb_python.fasta)
generate_unspliced_fasta() (in module kb_python.fasta)
get_bustools_binary_path() (in module kb_python.config)
get_bustools_version() (in module kb_python.utils)
get_kallisto_binary_path() (in module kb_python.config)
get_kallisto_version() (in module kb_python.utils)
get_supported_technologies() (in module kb_python.utils)
GROUP_PARSER (kb_python.fasta.FASTA attribute)
(kb_python.gtf.GTF attribute)
GTF (class in kb_python.gtf)
I
import_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)
INTRON_FILENAME (in module kb_python.constants)
K
kallisto_bus() (in module kb_python.count)
kallisto_index() (in module kb_python.ref)
kb_python (module)
kb_python.config (module)
kb_python.constants (module)
kb_python.count (module)
kb_python.fasta (module)
kb_python.gtf (module)
kb_python.main (module)
kb_python.ref (module)
kb_python.utils (module)
L
logger (in module kb_python.count)
(in module kb_python.fasta)
(in module kb_python.gtf)
(in module kb_python.ref)
(in module kb_python.utils)
M
main() (in module kb_python.main)
make_header() (kb_python.fasta.FASTA static method)
N
NotImplementedException
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_count() (in module kb_python.main)
parse_entry() (kb_python.gtf.GTF static method)
parse_header() (kb_python.fasta.FASTA static method)
parse_ref() (in module kb_python.main)
parse_technologies() (in module kb_python.utils)
PARSER (kb_python.fasta.FASTA attribute)
(kb_python.gtf.GTF attribute)
PLATFORM (in module kb_python.config)
R
ref() (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)
reverse_complement() (kb_python.fasta.FASTA static method)
run_chain() (in module kb_python.utils)
run_executable() (in module kb_python.utils)
S
setup_count_args() (in module kb_python.main)
setup_info_args() (in module kb_python.main)
setup_ref_args() (in module kb_python.main)
sort() (kb_python.fasta.FASTA method)
(kb_python.gtf.GTF method)
sort_fasta() (in module kb_python.ref)
sort_gtf() (in module kb_python.ref)
SORTED_FASTA_FILENAME (in module kb_python.constants)
SORTED_GTF_FILENAME (in module kb_python.constants)
stream_fastqs() (in module kb_python.count)
stream_file() (in module kb_python.utils)
sum_anndatas() (in module kb_python.utils)
T
TECHNOLOGIES (in module kb_python.config)
TECHNOLOGIES_MAPPING (in module kb_python.config)
Technology (in module kb_python.config)
TECHNOLOGY_PARSER (in module kb_python.utils)
TEMP_DIR (in module kb_python.config)
TXNAMES_FILENAME (in module kb_python.constants)
U
UNFILTERED_COUNTS_DIR (in module kb_python.constants)
UnmetDependencyException
UnsupportedOSException
V
VERSION_PARSER (in module kb_python.utils)
W
WHITELIST_DIR (in module kb_python.config)
WHITELIST_FILENAME (in module kb_python.constants)
whitelist_provided() (in module kb_python.utils)
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