Index

Symbols

--barcode sep241prep command line option --bc-from-file sep241prep command line option --blacklist sep241prep command line option --blacklisted-seqs sep241prep command line option --c1-cov sep241deconvolve command line option sep241prep command line option --c1-cov-for-memory-estimation sep241prep command line option --c1-dirichlet-prior sep241deconvolve command line option --c1-min-peak-size sep241peakcalling command line option --c1-smooth sep241peakcalling command line option --c2-cov sep241deconvolve command line option sep241prep command line option --c2-cov-for-memory-estimation sep241prep command line option --c2-dirichlet-prior sep241deconvolve command line option --c2-min-peak-size sep241peakcalling command line option --c2-smooth sep241peakcalling command line option --compiledir sep241deconvolve command line option sep241prep command line option --constrain sep241deconvolve command line option --cores sep241deconvolve command line option sep241peakcalling command line option sep241prep command line option --exclude-flipped sep241events command line option sep241mkbw command line option sep241mkdt command line option --force sep241events command line option sep241mkbw command line option sep241mkdt command line option sep241peakcalling command line option --fraction-in-peaks sep241peakcalling command line option --fraction-overlap sep241peakcalling command line option --help sep241deconvolve command line option sep241events command line option sep241mkbw command line option sep241mkdt command line option sep241peakcalling command line option sep241prep command line option --interval-overlap sep241prep command line option --kde-bw sep241prep command line option --kde-threshold sep241prep command line option --keep-duplicates sep241prep command line option --length-dist-mode-sds sep241deconvolve command line option --length-dist-modes sep241deconvolve command line option --log sep241deconvolve command line option sep241events command line option sep241mkbw command line option sep241mkdt command line option sep241peakcalling command line option sep241prep command line option --logfile sep241deconvolve command line option sep241events command line option sep241mkbw command line option sep241mkdt command line option sep241peakcalling command line option sep241prep command line option

--max-cuts sep241prep command line option --max-locs sep241prep command line option --memory-target sep241prep command line option --no-check sep241events command line option sep241mkbw command line option sep241mkdt command line option sep241peakcalling command line option --no-progress sep241events command line option sep241mkbw command line option sep241mkdt command line option sep241peakcalling command line option sep241prep command line option --omit-seqname-postfix sep241prep command line option --only-check sep241peakcalling command line option --out sep241events command line option sep241mkbw command line option sep241mkdt command line option sep241peakcalling command line option sep241prep command line option --region sep241mkbw command line option sep241mkdt command line option --region-padding sep241prep command line option --seed sep241prep command line option --selection-bed sep241prep command line option --selection-padding sep241prep command line option --span sep241mkbw command line option sep241mkdt command line option sep241peakcalling command line option --sparsity-threshold sep241deconvolve command line option sep241prep command line option --sparsity-threshold-for-memory-estimation sep241prep command line option --uncorrected sep241peakcalling command line option --unit sep241mkbw command line option sep241mkdt command line option --workchunk sep241deconvolve command line option -h sep241deconvolve command line option sep241events command line option sep241mkbw command line option sep241mkdt command line option sep241peakcalling command line option sep241prep command line option -l sep241deconvolve command line option sep241events command line option sep241mkbw command line option sep241mkdt command line option sep241peakcalling command line option sep241prep command line option -o sep241events command line option sep241mkbw command line option sep241mkdt command line option sep241peakcalling command line option sep241prep command line option

A

all_fragments() (sep241util.DataManager method)

ArgumentError auto_jitter() (sep241covariance.SparseCov method)

B

BadCovariance

BarcodeError BEDFormatError

C

check_length_distribution_flip() (in module sep241util) chrom-sizes-file sep241mkbw command line option sep241mkdt command line option

count() (sep241util.DataManager method)

D

DataManager (class in sep241util)

deconvolve() (in module sep241model) detect_cores() (in module sep241util)

E

envents_from_intervals() (sep241util.DataManager method)

F

file_length (sep241util.DataManager attribute) format_cuts() (in module sep241util)

fragment-file sep241prep command line option

G

get_cov_functions() (in module sep241model) get_fragments() (sep241util.DataManager method) get_free() (sep241util.LevelSet method) get_intervals() (sep241util.DataManager method)

get_length_dist_modes() (in module sep241model) gradient1_custom() (in module sep241model) gtf (sep241util.DataManager property) gtf_file (sep241util.DataManager property)

H

hist_from_df() (sep241util.DataManager method)

I

igv_plot() (in module sep241util)

J

jobdata-file sep241deconvolve command line option sep241events command line option sep241mkbw command line option sep241mkdt command line option sep241peakcalling command line option

L

length_dist() (in module sep241util)

length_histograms() (sep241util.DataManager method) LevelSet (class in sep241util)

M

make_bounds() (in module sep241model) make_model() (in module sep241model) MissingData module sep241covariance sep241latent sep241model sep241util

N

NoData, [1]

NotARegion

P

plot_frag_length() (sep241util.DataManager method) plot_genes() (sep241util.DataManager method) plot_gtf() (in module sep241util) plot_igv() (sep241util.DataManager method)

plot_length_hist() (sep241util.DataManager method) posterior_length_dists() (in module sep241util) posterior_mode_weights() (in module sep241util) prior() (sep241latent.SparseLatent method)

R

read_job_data() (in module sep241util) read_region_string() (in module sep241util)

read_results() (in module sep241util) reset() (sep241util.LevelSet method)

S

safety_check() (in module sep241model) sep241covariance module sep241deconvolve command line option --c1-cov --c1-dirichlet-prior --c2-cov --c2-dirichlet-prior --compiledir --constrain --cores --help --length-dist-mode-sds --length-dist-modes --log --logfile --sparsity-threshold --workchunk -h -l jobdata-file sep241events command line option --exclude-flipped --force --help --log --logfile --no-check --no-progress --out -h -l -o jobdata-file sep241latent module sep241mkbw command line option --exclude-flipped --force --help --log --logfile --no-check --no-progress --out --region --span --unit -h -l -o chrom-sizes-file jobdata-file sep241mkdt command line option --exclude-flipped --force --help --log --logfile --no-check --no-progress --out --region --span --unit -h -l -o chrom-sizes-file jobdata-file

sep241model module sep241peakcalling command line option --c1-min-peak-size --c1-smooth --c2-min-peak-size --c2-smooth --cores --force --fraction-in-peaks --fraction-overlap --help --log --logfile --no-check --no-progress --only-check --out --span --uncorrected -h -l -o jobdata-file sep241prep command line option --barcode --bc-from-file --blacklist --blacklisted-seqs --c1-cov --c1-cov-for-memory-estimation --c2-cov --c2-cov-for-memory-estimation --compiledir --cores --help --interval-overlap --kde-bw --kde-threshold --keep-duplicates --log --logfile --max-cuts --max-locs --memory-target --no-progress --omit-seqname-postfix --out --region-padding --seed --selection-bed --selection-padding --sparsity-threshold --sparsity-threshold-for-memory-estimation -h -l -o fragment-file sep241util module set_flag() (in module sep241util) setup_logging() (in module sep241util) SparseCov (class in sep241covariance) SparseLatent (class in sep241latent)

T

to_grouped_string() (in module sep241util)

W

write_bed() (in module sep241util)