prism
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Getting started
Getting started
What is PRISM?
How PRISM works
Installation
Requirements
Using PRISM
Using PRISM
Quickstart
Extract
Preprocess
Deconvolute
Scatter
Annotate
Related information
Related information
Citing PRISM
References
prism
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Index
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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H
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I
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J
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M
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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
B
BetaBinomialMixture (class in prism.mixture)
bic() (prism.mixture.BetaBinomialMixture method)
C
character_indices() (in module prism.extract)
common_intersection() (in module prism.deconvolute)
D
discard_noninformative_reads() (in module prism.extract)
dispersions_ (prism.mixture.BetaBinomialMixture attribute)
E
extend_region() (in module prism.extract)
extract_chromosome() (in module prism.util)
F
fit() (prism.mixture.BetaBinomialMixture method)
G
get_bam_handle() (in module prism.util)
get_binary_string_representation() (in module prism.util)
get_chromosome() (in module prism.deconvolute)
get_common_headers_by_jaccard_similarity() (in module prism.util)
get_counts() (prism.mixture.BetaBinomialMixture method)
get_cpg_coordinates() (in module prism.extract)
get_depths() (prism.mixture.BetaBinomialMixture method)
get_dispersions() (prism.mixture.BetaBinomialMixture method)
get_headers() (prism.mixture.BetaBinomialMixture method)
get_means() (prism.mixture.BetaBinomialMixture method)
get_n_components() (prism.mixture.BetaBinomialMixture method)
get_n_dimensions() (prism.mixture.BetaBinomialMixture method)
get_subclone_assignment() (in module prism.deconvolute)
get_weights() (prism.mixture.BetaBinomialMixture method)
H
has_overlap() (in module prism.extract)
hmm_proba() (in module prism.proofreading)
HMMModel (class in prism.hmm)
I
identify_subclone() (in module prism.deconvolute)
is_fully_methylated_or_unmethylated() (in module prism.util)
is_methylated() (in module prism.hmm)
J
jaccard_similarity() (in module prism.util)
M
mark_outlier_clusters() (in module prism.deconvolute)
means_ (prism.mixture.BetaBinomialMixture attribute)
merge_met_files() (in module prism.deconvolute)
merge_subclones() (in module prism.deconvolute)
merge_two_headers() (in module prism.util)
methylated_pattern() (in module prism.deconvolute)
O
overlaps() (in module prism.deconvolute)
P
param_generator() (in module prism.preprocess)
parse_cn_line() (in module prism.deconvolute)
parse_met_file() (in module prism.deconvolute)
parse_result_line() (in module prism.util)
pattern_counters_from_met() (in module prism.util)
postfiltered() (in module prism.deconvolute)
posthoc_process() (in module prism.deconvolute)
predict_proba() (prism.mixture.BetaBinomialMixture method)
prefiltered() (in module prism.preprocess)
prepare_header_bed() (in module prism.util)
preset_rc() (in module prism.util)
prism.annotate (module)
prism.deconvolute (module)
prism.extract (module)
prism.hmm (module)
prism.mixture (module)
prism.preprocess (module)
prism.proofreading (module)
prism.scatter (module)
prism.util (module)
proba() (prism.hmm.HMMModel method)
proofread() (in module prism.proofreading)
proofread_given_n_template() (in module prism.proofreading)
R
random_pattern() (in module prism.util)
Region (class in prism.util)
run() (in module prism.annotate)
(in module prism.deconvolute)
(in module prism.extract)
(in module prism.preprocess)
(in module prism.scatter)
S
save_met_file() (in module prism.extract)
scatter_1d() (in module prism.annotate)
(in module prism.scatter)
scatter_2d() (in module prism.annotate)
(in module prism.scatter)
T
trigamma() (in module prism.mixture)
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