dynast
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Introduction:
Getting started
Contents:
Pipeline Usage
Technical Information
API
References
Tutorials:
NASC-seq
scSLAM-seq
scNT-seq
sci-fate
dynast
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Index
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Index
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C
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D
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E
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F
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G
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I
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N
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P
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R
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W
_
__enter__() (dynast.utils.suppress_stdout_stderr method)
__exit__() (dynast.utils.suppress_stdout_stderr method)
__model (in module dynast.benchmarking.simulation)
__version__ (in module dynast)
_model (in module dynast.estimation.pi)
_pi_model (in module dynast.benchmarking.simulation)
_simulate() (in module dynast.benchmarking.simulation)
A
ADATA_FILENAME (in module dynast.constants)
aggregate_counts() (in module dynast.preprocessing)
(in module dynast.preprocessing.aggregation)
AGGREGATE_FILENAME (in module dynast.constants)
align() (in module dynast.align)
ALIGNMENT_COLUMNS (in module dynast.preprocessing.bam)
ALIGNMENTS_FILENAME (in module dynast.constants)
ALIGNMENTS_PARSER (in module dynast.preprocessing.conversion)
all_exists (in module dynast.utils)
arguments_to_list() (in module dynast.utils)
as_completed_with_progress() (in module dynast.utils)
B
BAM_BARCODE_TAG (in module dynast.config)
BAM_CONSENSUS_READ_COUNT_TAG (in module dynast.config)
BAM_GENE_TAG (in module dynast.config)
BAM_PEEK_READS (in module dynast.config)
BAM_READGROUP_TAG (in module dynast.config)
BAM_REQUIRED_TAGS (in module dynast.config)
BAM_STRAND_PARSER (in module dynast.technology)
BAM_UMI_TAG (in module dynast.config)
BARCODE_UMI_TECHNOLOGIES (in module dynast.technology)
BASE_COLUMNS (in module dynast.preprocessing.conversion)
BASE_IDX (in module dynast.preprocessing.consensus)
(in module dynast.preprocessing.conversion)
BASES (in module dynast.preprocessing.consensus)
beta_mean() (in module dynast.estimation.pi)
beta_mode() (in module dynast.estimation.pi)
binomial_pmf() (in module dynast.estimation.p_c)
BINS_DIR (in module dynast.config)
C
calculate_coverage() (in module dynast.preprocessing)
(in module dynast.preprocessing.coverage)
calculate_coverage_contig() (in module dynast.preprocessing.coverage)
calculate_mutation_rates() (in module dynast.preprocessing)
(in module dynast.preprocessing.aggregation)
call_consensus() (in module dynast.preprocessing)
(in module dynast.preprocessing.consensus)
call_consensus_from_reads() (in module dynast.preprocessing.consensus)
call_consensus_from_reads_process() (in module dynast.preprocessing.consensus)
check_bam_contains_duplicate() (in module dynast.preprocessing)
(in module dynast.preprocessing.bam)
check_bam_contains_secondary() (in module dynast.preprocessing)
(in module dynast.preprocessing.bam)
check_bam_contains_unmapped() (in module dynast.preprocessing)
(in module dynast.preprocessing.bam)
check_bam_is_paired() (in module dynast.preprocessing.bam)
check_bam_tags_exist() (in module dynast.preprocessing.bam)
COLUMNS (in module dynast.preprocessing.conversion)
combine_arguments() (in module dynast.utils)
COMMAND_TO_FUNCTION (in module dynast.main)
complement_counts() (in module dynast.preprocessing)
(in module dynast.preprocessing.conversion)
consensus() (in module dynast.consensus)
CONSENSUS_BAM_FILENAME (in module dynast.constants)
consensus_worker() (in module dynast.preprocessing.consensus)
CONVERSION_COLUMNS (in module dynast.preprocessing.conversion)
CONVERSION_COMPLEMENT (in module dynast.preprocessing)
(in module dynast.preprocessing.conversion)
CONVERSION_CSV_COLUMNS (in module dynast.preprocessing.bam)
CONVERSION_IDX (in module dynast.preprocessing.conversion)
CONVERSIONS_FILENAME (in module dynast.constants)
CONVERSIONS_INDEX_FILENAME (in module dynast.constants)
CONVERSIONS_PARSER (in module dynast.preprocessing.conversion)
CONVS_FILENAME (in module dynast.constants)
count() (in module dynast.count)
count_conversions() (in module dynast.preprocessing)
(in module dynast.preprocessing.conversion)
count_conversions_part() (in module dynast.preprocessing.conversion)
COUNT_DIR (in module dynast.constants)
count_no_conversions() (in module dynast.preprocessing.conversion)
COUNTS_PREFIX (in module dynast.constants)
COUNTS_SPLIT_THRESHOLD (in module dynast.config)
counts_to_matrix() (in module dynast.utils)
COVERAGE_FILENAME (in module dynast.constants)
COVERAGE_INDEX_FILENAME (in module dynast.constants)
COVERAGE_PARSER (in module dynast.preprocessing.coverage)
CSV_COLUMNS (in module dynast.preprocessing.conversion)
D
decompress_gzip (in module dynast.utils)
deduplicate_counts() (in module dynast.preprocessing)
(in module dynast.preprocessing.conversion)
deduplicate_counts_part() (in module dynast.preprocessing.conversion)
detect_snps() (in module dynast.preprocessing)
(in module dynast.preprocessing.snp)
detect_strand() (in module dynast.technology)
dict_to_matrix() (in module dynast.utils)
display_progress_with_counter() (in module dynast.utils)
downsample_counts() (in module dynast.utils)
drop_multimappers() (in module dynast.preprocessing.conversion)
drop_multimappers_part() (in module dynast.preprocessing.conversion)
dynast
module
dynast.align
module
dynast.benchmarking
module
dynast.benchmarking.simulation
module
dynast.config
module
dynast.consensus
module
dynast.constants
module
dynast.count
module
dynast.estimate
module
dynast.estimation
module
dynast.estimation.alpha
module
dynast.estimation.p_c
module
dynast.estimation.p_e
module
dynast.estimation.pi
module
dynast.logging
module
dynast.main
module
dynast.preprocessing
module
dynast.preprocessing.aggregation
module
dynast.preprocessing.bam
module
dynast.preprocessing.consensus
module
dynast.preprocessing.conversion
module
dynast.preprocessing.coverage
module
dynast.preprocessing.snp
module
dynast.ref
module
dynast.stats
module
dynast.technology
module
dynast.utils
module
E
end() (dynast.stats.Stats method)
(dynast.stats.Step method)
estimate() (in module dynast.benchmarking.simulation)
(in module dynast.estimate)
estimate_alpha() (in module dynast.estimation)
(in module dynast.estimation.alpha)
ESTIMATE_DIR (in module dynast.constants)
estimate_p_c() (in module dynast.estimation)
(in module dynast.estimation.p_c)
estimate_p_e() (in module dynast.estimation)
(in module dynast.estimation.p_e)
estimate_p_e_control() (in module dynast.estimation)
(in module dynast.estimation.p_e)
estimate_p_e_nasc() (in module dynast.estimation)
(in module dynast.estimation.p_e)
estimate_pi() (in module dynast.estimation)
(in module dynast.estimation.pi)
expectation_maximization() (in module dynast.estimation.p_c)
expectation_maximization_nasc() (in module dynast.estimation.p_c)
extract_conversions() (in module dynast.preprocessing.snp)
extract_conversions_part() (in module dynast.preprocessing.snp)
F
fit_stan_mcmc() (in module dynast.estimation.pi)
flatten_dict_values (in module dynast.utils)
flatten_dictionary (in module dynast.utils)
flatten_iter (in module dynast.utils)
G
generate_sequence() (in module dynast.benchmarking.simulation)
GENES_FILENAME (in module dynast.constants)
get_available_memory() (in module dynast.utils)
get_file_descriptor_limit() (in module dynast.utils)
get_max_file_descriptor_limit() (in module dynast.utils)
get_STAR_binary_path() (in module dynast.utils)
get_STAR_version() (in module dynast.utils)
get_tags_from_bam() (in module dynast.preprocessing)
(in module dynast.preprocessing.bam)
guess_beta_parameters() (in module dynast.estimation.pi)
I
increase_file_descriptor_limit() (in module dynast.utils)
initializer() (in module dynast.benchmarking.simulation)
(in module dynast.estimation.pi)
L
logger (in module dynast.logging)
M
main() (in module dynast.main)
make_pool_with_counter() (in module dynast.utils)
merge_aggregates() (in module dynast.preprocessing)
(in module dynast.preprocessing.aggregation)
merge_dictionaries (in module dynast.utils)
mkstemp (in module dynast.utils)
MODEL_NAME (in module dynast.config)
MODEL_PATH (in module dynast.config)
MODELS_DIR (in module dynast.config)
module
dynast
dynast.align
dynast.benchmarking
dynast.benchmarking.simulation
dynast.config
dynast.consensus
dynast.constants
dynast.count
dynast.estimate
dynast.estimation
dynast.estimation.alpha
dynast.estimation.p_c
dynast.estimation.p_e
dynast.estimation.pi
dynast.logging
dynast.main
dynast.preprocessing
dynast.preprocessing.aggregation
dynast.preprocessing.bam
dynast.preprocessing.consensus
dynast.preprocessing.conversion
dynast.preprocessing.coverage
dynast.preprocessing.snp
dynast.ref
dynast.stats
dynast.technology
dynast.utils
N
NASC_ARGUMENTS (in module dynast.config)
O
open_as_text (in module dynast.utils)
P
P_C_PREFIX (in module dynast.constants)
P_E_FILENAME (in module dynast.constants)
PACKAGE_PATH (in module dynast.config)
parse_align() (in module dynast.main)
parse_all_reads() (in module dynast.preprocessing)
(in module dynast.preprocessing.bam)
parse_consensus() (in module dynast.main)
parse_count() (in module dynast.main)
PARSE_DIR (in module dynast.constants)
parse_estimate() (in module dynast.main)
parse_read_contig() (in module dynast.preprocessing.bam)
parse_ref() (in module dynast.main)
patch_mp_connection_bpo_17560() (in module dynast.utils)
PLATE_TECHNOLOGIES (in module dynast.technology)
PLATFORM (in module dynast.config)
plot_estimations() (in module dynast.benchmarking.simulation)
print_technologies() (in module dynast.main)
R
RATES_PREFIX (in module dynast.constants)
read_aggregates() (in module dynast.preprocessing)
(in module dynast.preprocessing.aggregation)
read_alignments() (in module dynast.preprocessing)
(in module dynast.preprocessing.bam)
read_alpha() (in module dynast.estimation)
(in module dynast.estimation.alpha)
read_conversions() (in module dynast.preprocessing)
(in module dynast.preprocessing.bam)
read_counts() (in module dynast.preprocessing)
(in module dynast.preprocessing.conversion)
read_coverage() (in module dynast.preprocessing)
(in module dynast.preprocessing.coverage)
read_p_c() (in module dynast.estimation)
(in module dynast.estimation.p_c)
read_p_e() (in module dynast.estimation)
(in module dynast.estimation.p_e)
read_pi() (in module dynast.estimation)
(in module dynast.estimation.pi)
read_pickle (in module dynast.utils)
read_rates() (in module dynast.preprocessing)
(in module dynast.preprocessing.aggregation)
read_snp_csv() (in module dynast.preprocessing)
(in module dynast.preprocessing.snp)
read_snps() (in module dynast.preprocessing)
(in module dynast.preprocessing.snp)
RECOMMENDED_MEMORY (in module dynast.config)
ref() (in module dynast.ref)
results_to_adata() (in module dynast.utils)
run_executable (in module dynast.utils)
S
save() (dynast.stats.Stats method)
select_alignments() (in module dynast.preprocessing)
(in module dynast.preprocessing.bam)
setup_align_args() (in module dynast.main)
setup_consensus_args() (in module dynast.main)
setup_count_args() (in module dynast.main)
setup_estimate_args() (in module dynast.main)
setup_ref_args() (in module dynast.main)
simulate() (in module dynast.benchmarking.simulation)
simulate_batch() (in module dynast.benchmarking.simulation)
simulate_reads() (in module dynast.benchmarking.simulation)
SNP_COLUMNS (in module dynast.preprocessing.snp)
SNPS_FILENAME (in module dynast.constants)
sort_and_index_bam() (in module dynast.preprocessing)
(in module dynast.preprocessing.bam)
split_bam() (in module dynast.preprocessing.bam)
split_counts() (in module dynast.utils)
split_counts_by_velocity() (in module dynast.preprocessing)
(in module dynast.preprocessing.conversion)
split_index() (in module dynast.utils)
split_matrix_alpha() (in module dynast.utils)
split_matrix_pi() (in module dynast.utils)
STAR_ARGUMENTS (in module dynast.config)
STAR_BAI_FILENAME (in module dynast.constants)
STAR_BAM_FILENAME (in module dynast.constants)
STAR_BARCODES_FILENAME (in module dynast.constants)
STAR_FEATURES_FILENAME (in module dynast.constants)
STAR_FILTERED_DIR (in module dynast.constants)
STAR_GENE_DIR (in module dynast.constants)
STAR_genomeGenerate() (in module dynast.ref)
STAR_MATRIX_FILENAME (in module dynast.constants)
STAR_RAW_DIR (in module dynast.constants)
STAR_solo() (in module dynast.align)
STAR_SOLO_ARGUMENTS (in module dynast.config)
STAR_SOLO_DIR (in module dynast.constants)
STAR_VELOCYTO_DIR (in module dynast.constants)
start() (dynast.stats.Stats method)
(dynast.stats.Step method)
Stats (class in dynast.stats)
STATS_PREFIX (in module dynast.constants)
Step (class in dynast.stats)
step() (dynast.stats.Stats method)
STRAND_MAP (in module dynast.technology)
subset_counts() (in module dynast.preprocessing)
(in module dynast.preprocessing.conversion)
suppress_stdout_stderr (class in dynast.utils)
T
TECHNOLOGIES (in module dynast.technology)
TECHNOLOGIES_MAP (in module dynast.technology)
Technology (in module dynast.technology)
to_dict() (dynast.stats.Stats method)
(dynast.stats.Step method)
U
UnsupportedOSException
V
VELOCITY_BLACKLIST (in module dynast.config)
W
write_pickle (in module dynast.utils)
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