k-seq
Installation
Getting Started Tutorial
k-seq
package
k-seq
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Index
Index
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A
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B
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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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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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X
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Y
_
__init__() (k_seq.data.grouper.Grouper method)
(k_seq.data.seq_data.SeqData method)
(k_seq.data.seq_data.SeqTable method)
(k_seq.data.simu.SimulationResults method)
(k_seq.estimate.bootstrap.Bootstrap method)
(k_seq.estimate.convergence.ConvergenceTester method)
(k_seq.estimate.least_squares.FitResults method)
(k_seq.estimate.least_squares.SingleFitter method)
(k_seq.estimate.least_squares_batch.BatchFitResults method)
,
[1]
(k_seq.estimate.least_squares_batch.BatchFitter method)
,
[1]
(k_seq.model.pool.PoolModel method)
(k_seq.utility.func_tools.AttrScope method)
A
about() (k_seq.data.seq_data.SeqTable method)
add() (k_seq.data.grouper.GrouperCollection method)
(k_seq.utility.func_tools.AttrScope method)
add_grouper() (k_seq.data.seq_data.SeqData method)
add_sample_total() (k_seq.data.seq_data.SeqData method)
add_spike_in() (k_seq.data.seq_data.SeqData method)
amount_first_order() (k_seq.model.kinetic.BYOModel static method)
AttrScope (class in k_seq.utility.func_tools)
ax_none() (in module k_seq.utility.plot_tools)
axis (k_seq.data.grouper.Grouper attribute)
axis_mapper() (in module k_seq.data)
B
barplot() (in module k_seq.utility.plot_tools)
BatchFitResults (class in k_seq.estimate.least_squares_batch)
,
[1]
BatchFitter (class in k_seq.estimate.least_squares_batch)
,
[1]
BLUE (k_seq.utility.plot_tools.color attribute)
blue_header() (in module k_seq.utility.plot_tools)
BOLD (k_seq.utility.plot_tools.color attribute)
Bootstrap (class in k_seq.estimate.bootstrap)
bootstrap (k_seq.estimate.least_squares.SingleFitter attribute)
bootstrap_config (k_seq.estimate.least_squares.SingleFitter attribute)
bootstrap_num (k_seq.estimate.bootstrap.Bootstrap attribute)
(k_seq.estimate.least_squares.SingleFitter attribute)
bounds (k_seq.estimate.least_squares.SingleFitter attribute)
bs_method (k_seq.estimate.bootstrap.Bootstrap attribute)
(k_seq.estimate.least_squares.SingleFitter attribute)
bs_method() (k_seq.estimate.bootstrap.Bootstrap property)
bs_record() (k_seq.estimate.least_squares_batch.BatchFitResults method)
,
[1]
,
[2]
,
[3]
bs_record_num (k_seq.estimate.bootstrap.Bootstrap attribute)
(k_seq.estimate.least_squares.SingleFitter attribute)
bs_stats (k_seq.estimate.bootstrap.Bootstrap attribute)
BYOModel (class in k_seq.model.kinetic)
C
check_attr_value() (in module k_seq.utility.func_tools)
check_dir() (in module k_seq.utility.file_tools)
check_scalar() (in module k_seq.model.kinetic)
color (class in k_seq.utility.plot_tools)
color_cat10() (k_seq.utility.plot_tools.Presets static method)
color_pastel1() (k_seq.utility.plot_tools.Presets static method)
color_tab10() (k_seq.utility.plot_tools.Presets static method)
combination() (in module k_seq.data.variant_pool)
compo_lognormal() (k_seq.data.simu.DistGenerators static method)
composition_first_order() (k_seq.model.kinetic.BYOModel static method)
config (k_seq.estimate.least_squares.SingleFitter attribute)
conv_init_range (k_seq.estimate.convergence.ConvergenceTester attribute)
conv_record() (k_seq.estimate.least_squares_batch.BatchFitResults method)
,
[1]
,
[2]
,
[3]
conv_reps (k_seq.estimate.convergence.ConvergenceTester attribute)
conv_stats (k_seq.estimate.convergence.ConvergenceTester attribute)
convergence (k_seq.estimate.least_squares.FitResults attribute)
convergence_test() (k_seq.estimate.least_squares.SingleFitter method)
ConvergenceTester (class in k_seq.estimate.convergence)
count_model (k_seq.model.pool.PoolModel attribute)
count_params (k_seq.model.pool.PoolModel attribute)
cross_table_compare() (in module k_seq.data.seq_data_analyzer)
curve_fit_kwargs (k_seq.estimate.least_squares.SingleFitter attribute)
CYAN (k_seq.utility.plot_tools.color attribute)
D
d_mutant_fraction() (in module k_seq.data.variant_pool)
DARKCYAN (k_seq.utility.plot_tools.color attribute)
data (k_seq.estimate.least_squares.FitResults attribute)
(k_seq.estimate.least_squares_batch.BatchFitResults attribute)
,
[1]
density() (k_seq.data.seq_data.SeqTable property)
describe() (k_seq.data.seq_data.SeqTable method)
dict_flatten() (in module k_seq.utility.func_tools)
DistGenerators (class in k_seq.data.simu)
dump_json() (in module k_seq.utility.file_tools)
dump_pickle() (in module k_seq.utility.file_tools)
E
END (k_seq.utility.plot_tools.color attribute)
estimator (k_seq.estimate.bootstrap.Bootstrap attribute)
(k_seq.estimate.convergence.ConvergenceTester attribute)
(k_seq.estimate.least_squares.FitResults attribute)
(k_seq.estimate.least_squares_batch.BatchFitResults attribute)
,
[1]
exclude_zero (k_seq.estimate.least_squares.SingleFitter attribute)
extract_metadata() (in module k_seq.utility.file_tools)
F
fastq_to_count() (in module k_seq.data.preprocess)
filter_axis() (k_seq.data.seq_data.SeqTable method)
first_order() (in module k_seq.model.kinetic)
fit() (k_seq.estimate.least_squares.SingleFitter method)
(k_seq.estimate.least_squares_batch.BatchFitter method)
,
[1]
(k_seq.estimate.model_ident.ParamMap method)
fit_params (k_seq.estimate.least_squares_batch.BatchFitter attribute)
,
[1]
FitResults (class in k_seq.estimate.least_squares)
format_ticks() (in module k_seq.utility.plot_tools)
from_count_files() (k_seq.data.seq_data.SeqData static method)
from_json() (k_seq.data.seq_data.SeqData method)
(k_seq.estimate.least_squares.FitResults class method)
(k_seq.estimate.least_squares.SingleFitter class method)
(k_seq.estimate.least_squares_batch.BatchFitResults class method)
,
[1]
(k_seq.estimate.least_squares_batch.BatchFitResults method)
,
[1]
from_list() (k_seq.utility.plot_tools.Presets static method)
from_pickle() (k_seq.data.seq_data.SeqData static method)
(k_seq.estimate.least_squares_batch.BatchFitResults class method)
,
[1]
(k_seq.estimate.least_squares_batch.BatchFitResults method)
,
[1]
func() (k_seq.model.ModelBase method)
(k_seq.model.pool.PoolModel method)
FuncToMethod (class in k_seq.utility.func_tools)
G
gamma() (in module k_seq.estimate.model_ident)
generate_summary() (k_seq.estimate.least_squares_batch.BatchFitResults static method)
,
[1]
get_est_results() (k_seq.data.simu.SimulationResults method)
get_file_list() (in module k_seq.utility.file_tools)
get_FitResult() (k_seq.estimate.least_squares_batch.BatchFitResults method)
,
[1]
get_fold_range() (k_seq.data.simu.SimulationResults method)
get_func_params() (in module k_seq.utility.func_tools)
get_group() (in module k_seq.data.grouper)
get_metric_values() (k_seq.estimate.model_ident.ParamMap method)
get_pct_gaussian_error() (in module k_seq.data.simu)
get_table() (k_seq.data.grouper.Grouper method)
get_uncertainty_accuracy() (k_seq.data.simu.SimulationResults method)
GREEN (k_seq.utility.plot_tools.color attribute)
group (k_seq.data.grouper.Grouper attribute)
Grouper (class in k_seq.data.grouper)
grouper (k_seq.estimate.bootstrap.Bootstrap attribute)
GrouperCollection (class in k_seq.data.grouper)
I
init_guess (k_seq.estimate.least_squares.SingleFitter attribute)
is_int() (in module k_seq.utility.func_tools)
is_numeric() (in module k_seq.utility.func_tools)
is_sparse() (in module k_seq.utility.func_tools)
K
k_seq.data
module
k_seq.data.grouper
module
k_seq.data.preprocess
module
k_seq.data.seq_data
module
k_seq.data.seq_data_analyzer
module
k_seq.data.simu
module
k_seq.data.variant_pool
module
k_seq.estimate
module
k_seq.estimate.bootstrap
module
k_seq.estimate.convergence
module
k_seq.estimate.least_squares
module
k_seq.estimate.least_squares_batch
module
,
[1]
k_seq.estimate.model_ident
module
k_seq.estimate.replicates
module
k_seq.model
module
k_seq.model.count
module
k_seq.model.kinetic
module
k_seq.model.pool
module
k_seq.utility
module
k_seq.utility.file_tools
module
k_seq.utility.func_tools
module
k_seq.utility.plot_tools
module
kendall_log() (in module k_seq.estimate.model_ident)
kinetic_model (k_seq.model.pool.PoolModel attribute)
kinetic_params (k_seq.model.pool.PoolModel attribute)
L
large_data (k_seq.estimate.least_squares_batch.BatchFitResults attribute)
,
[1]
load_model() (k_seq.estimate.least_squares_batch.BatchFitter class method)
,
[1]
load_result() (k_seq.estimate.least_squares_batch.BatchFitResults class method)
,
[1]
(k_seq.estimate.least_squares_batch.BatchFitResults method)
,
[1]
(k_seq.estimate.model_ident.ParamMap class method)
load_Seqtable_from_count_files() (in module k_seq.data.preprocess)
load_tar_gz() (in module k_seq.utility.file_tools)
lognormal() (k_seq.data.simu.DistGenerators static method)
M
markers() (k_seq.utility.plot_tools.Presets static method)
metric (k_seq.estimate.least_squares.SingleFitter attribute)
model (k_seq.estimate.least_squares.FitResults attribute)
(k_seq.estimate.least_squares.SingleFitter attribute)
(k_seq.estimate.least_squares_batch.BatchFitResults attribute)
,
[1]
(k_seq.estimate.least_squares_batch.BatchFitter attribute)
,
[1]
ModelBase (class in k_seq.model)
module
k_seq.data
k_seq.data.grouper
k_seq.data.preprocess
k_seq.data.seq_data
k_seq.data.seq_data_analyzer
k_seq.data.simu
k_seq.data.variant_pool
k_seq.estimate
k_seq.estimate.bootstrap
k_seq.estimate.convergence
k_seq.estimate.least_squares
k_seq.estimate.least_squares_batch
,
[1]
k_seq.estimate.model_ident
k_seq.estimate.replicates
k_seq.model
k_seq.model.count
k_seq.model.kinetic
k_seq.model.pool
k_seq.utility
k_seq.utility.file_tools
k_seq.utility.func_tools
k_seq.utility.plot_tools
mp_job() (in module k_seq.utility)
multinomial() (in module k_seq.model.count)
N
n_replicates() (k_seq.estimate.replicates.Replicates property)
name (k_seq.estimate.least_squares.SingleFitter attribute)
neighbor_effect_error() (in module k_seq.data.variant_pool)
neighbor_effect_observation() (in module k_seq.data.variant_pool)
note (k_seq.estimate.least_squares_batch.BatchFitter attribute)
,
[1]
(k_seq.model.pool.PoolModel attribute)
num_of_seq() (in module k_seq.data.variant_pool)
O
opt_method (k_seq.estimate.least_squares.SingleFitter attribute)
P
pairplot() (in module k_seq.utility.plot_tools)
param_to_dict() (in module k_seq.utility.func_tools)
parameter (k_seq.estimate.least_squares.SingleFitter attribute)
ParamMap (class in k_seq.estimate.model_ident)
pearson() (in module k_seq.estimate.model_ident)
pearson_log() (in module k_seq.estimate.model_ident)
plot_curve() (in module k_seq.utility.plot_tools)
plot_fitting_curves() (k_seq.estimate.least_squares.FitResults method)
plot_loss_heatmap() (in module k_seq.utility.plot_tools)
(k_seq.estimate.least_squares.FitResults method)
plot_map() (k_seq.estimate.model_ident.ParamMap method)
point_estimate() (k_seq.estimate.least_squares.SingleFitter method)
point_estimation (k_seq.estimate.least_squares.FitResults attribute)
PoolModel (class in k_seq.model.pool)
PoolParamGenerator (class in k_seq.data.simu)
predict() (k_seq.model.ModelBase method)
(k_seq.model.pool.PoolModel method)
Presets (class in k_seq.utility.plot_tools)
PURPLE (k_seq.utility.plot_tools.color attribute)
R
reacted_frac() (k_seq.model.kinetic.BYOModel static method)
read_count_file() (in module k_seq.data.preprocess)
read_json() (in module k_seq.utility.file_tools)
read_pickle() (in module k_seq.utility.file_tools)
read_table_files() (in module k_seq.utility.file_tools)
record_full (k_seq.estimate.bootstrap.Bootstrap attribute)
RED (k_seq.utility.plot_tools.color attribute)
regplot() (in module k_seq.utility.plot_tools)
remove_nan() (in module k_seq.estimate.model_ident)
rep_variance_scatter() (in module k_seq.data.seq_data_analyzer)
Replicates (class in k_seq.estimate.replicates)
results (k_seq.estimate.least_squares.SingleFitter attribute)
(k_seq.estimate.least_squares_batch.BatchFitter attribute)
,
[1]
rnd_seed (k_seq.estimate.least_squares.SingleFitter attribute)
run() (k_seq.estimate.bootstrap.Bootstrap method)
(k_seq.estimate.convergence.ConvergenceTester method)
,
[1]
(k_seq.estimate.replicates.Replicates method)
run_bootstrap() (k_seq.estimate.least_squares.SingleFitter method)
run_replicates() (k_seq.estimate.least_squares.SingleFitter method)
run_subprocess() (in module k_seq.utility.func_tools)
S
sample_entropy_scatterplot() (in module k_seq.data.seq_data_analyzer)
sample_from_dataframe() (k_seq.data.simu.PoolParamGenerator class method)
sample_from_iid_dist() (k_seq.data.simu.PoolParamGenerator static method)
sample_info() (in module k_seq.data.seq_data_analyzer)
sample_overview() (in module k_seq.data.seq_data_analyzer)
sample_overview_plots() (in module k_seq.data.seq_data_analyzer)
sample_rel_abun_hist() (in module k_seq.data.seq_data_analyzer)
sample_spike_in_ratio_scatterplot() (in module k_seq.data.seq_data_analyzer)
sample_total_reads_barplot() (in module k_seq.data.seq_data_analyzer)
sample_unique_seqs_barplot() (in module k_seq.data.seq_data_analyzer)
samples() (k_seq.data.seq_data.SeqData property)
(k_seq.data.seq_data.SeqTable property)
save_model() (k_seq.estimate.least_squares_batch.BatchFitter method)
,
[1]
save_results() (k_seq.estimate.least_squares_batch.BatchFitter method)
,
[1]
save_to() (k_seq.estimate.least_squares_batch.BatchFitter property)
,
[1]
savefig() (in module k_seq.utility.plot_tools)
seq_length_dist() (in module k_seq.data.seq_data_analyzer)
seq_mean_value_detected_samples_scatterplot() (in module k_seq.data.seq_data_analyzer)
seq_overview() (in module k_seq.data.seq_data_analyzer)
seq_table (k_seq.data.seq_data.SeqData attribute)
seq_to_fit (k_seq.estimate.least_squares_batch.BatchFitter attribute)
,
[1]
seq_variance() (in module k_seq.data.seq_data_analyzer)
SeqData (class in k_seq.data.seq_data)
SeqDataAnalyzer (class in k_seq.data.seq_data_analyzer)
seqs() (k_seq.data.seq_data.SeqData property)
(k_seq.data.seq_data.SeqTable property)
SeqTable (class in k_seq.data.seq_data)
SeqTableAnalyzer (class in k_seq.data.seq_data_analyzer)
sigma (k_seq.estimate.least_squares.SingleFitter attribute)
(k_seq.estimate.least_squares_batch.BatchFitter attribute)
,
[1]
silent (k_seq.estimate.least_squares.SingleFitter attribute)
simulate_counts() (in module k_seq.data.simu)
simulate_on_byo_doped_condition_from_exp_results() (in module k_seq.data.simu)
simulate_samples() (k_seq.estimate.model_ident.ParamMap method)
simulate_w_byo_doped_condition_from_param_dist() (in module k_seq.data.simu)
SimulationResults (class in k_seq.data.simu)
SingleFitter (class in k_seq.estimate.least_squares)
slice_table() (in module k_seq.data.seq_data)
spearman() (in module k_seq.estimate.model_ident)
spearman_log() (in module k_seq.estimate.model_ident)
split() (k_seq.data.grouper.Grouper method)
summary (k_seq.estimate.least_squares_batch.BatchFitResults attribute)
,
[1]
summary() (k_seq.estimate.least_squares.SingleFitter method)
(k_seq.estimate.least_squares_batch.BatchFitter method)
,
[1]
summary_to_csv() (k_seq.estimate.least_squares_batch.BatchFitResults method)
,
[1]
,
[2]
,
[3]
T
table_object_to_dataframe() (in module k_seq.utility.file_tools)
target (k_seq.data.grouper.Grouper attribute)
to_dict() (k_seq.estimate.least_squares.SingleFitter method)
to_json() (k_seq.data.seq_data.SeqData method)
(k_seq.estimate.least_squares.FitResults method)
(k_seq.estimate.least_squares.SingleFitter method)
(k_seq.estimate.least_squares_batch.BatchFitResults method)
,
[1]
,
[2]
,
[3]
to_pickle() (k_seq.data.seq_data.SeqData method)
(k_seq.estimate.least_squares_batch.BatchFitResults method)
,
[1]
,
[2]
,
[3]
to_scalar() (in module k_seq.model.kinetic)
to_series() (k_seq.estimate.least_squares.FitResults method)
type (k_seq.data.grouper.Grouper attribute)
U
uncertainty (k_seq.estimate.least_squares.FitResults attribute)
UNDERLINE (k_seq.utility.plot_tools.color attribute)
uniform() (k_seq.data.simu.DistGenerators static method)
update_analysis() (k_seq.data.seq_data.SeqData method)
(k_seq.data.seq_data.SeqTable method)
update_none() (in module k_seq.utility.func_tools)
V
value_to_loc() (in module k_seq.utility.plot_tools)
X
x_data (k_seq.estimate.least_squares.SingleFitter attribute)
(k_seq.estimate.least_squares_batch.BatchFitter attribute)
,
[1]
Y
y_data (k_seq.estimate.least_squares.SingleFitter attribute)
y_dataframe (k_seq.estimate.least_squares_batch.BatchFitter attribute)
,
[1]
YELLOW (k_seq.utility.plot_tools.color attribute)