OncodriveFML
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OncodriveFML
OncodriveFML
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Analysis
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Behind the scenes
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Code documentation
oncodrivefml
OncodriveFML
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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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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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Q
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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
A
add_background() (oncodrivefml.executors.sig2probs.GroupSignature method)
(oncodrivefml.executors.sig2probs.NoSignature method)
(oncodrivefml.executors.sig2probs.SubstitutionProbs method)
add_observed() (oncodrivefml.executors.sig2probs.GroupSignature method)
(oncodrivefml.executors.sig2probs.SubstitutionProbs method)
add_search_widget() (oncodrivefml.store.QQPlot method)
add_symbol() (in module oncodrivefml.store)
add_tooltip() (oncodrivefml.store.QQPlot method)
add_tooltip_enhanced() (oncodrivefml.store.QQPlot method)
alt (oncodrivefml.scores.ScoreValue attribute)
ArithmeticMean (class in oncodrivefml.stats)
ArithmeticMeanHeteroscedasticScores (class in oncodrivefml.stats)
B
BIT_TO_REF (oncodrivefml.scores.PackScoresReader attribute)
build() (in module oncodrivefml.executors.sig2probs)
build_regions_tree() (in module oncodrivefml.load)
C
calc() (oncodrivefml.stats.ArithmeticMean static method)
(oncodrivefml.stats.GeometricMean static method)
(oncodrivefml.stats.Maximum static method)
calc_observed() (oncodrivefml.stats.ArithmeticMean static method)
(oncodrivefml.stats.ArithmeticMeanHeteroscedasticScores static method)
(oncodrivefml.stats.GeometricMean static method)
(oncodrivefml.stats.Maximum static method)
change (oncodrivefml.scores.ScoreValue attribute)
change_build() (in module oncodrivefml.reference)
choose() (oncodrivefml.indels.StopsScore method)
collapse() (in module oncodrivefml.signature)
compute() (in module oncodrivefml.signature)
compute_scores() (oncodrivefml.indels.Indel method)
count_valid_trinucleotides() (in module oncodrivefml.reference)
D
defaultdict_list() (in module oncodrivefml.utils)
E
eliminate_duplicates() (in module oncodrivefml.store)
executor_run() (in module oncodrivefml.utils)
exists_path() (in module oncodrivefml.utils)
F
function() (oncodrivefml.indels.StopsScore method)
G
GeometricMean (class in oncodrivefml.stats)
get() (oncodrivefml.scores.PackScoresReader method)
(oncodrivefml.scores.ScoresTabixReader method)
get_all_positions() (oncodrivefml.scores.Scores method)
get_background_indel_scores_as_stops() (oncodrivefml.indels.Indel method)
get_background_indel_scores_as_substitutions_without_signature() (oncodrivefml.indels.Indel method)
get_build() (in module oncodrivefml.reference)
get_indel_score_from_stop() (oncodrivefml.indels.Indel method)
get_indel_score_max_of_subs() (oncodrivefml.indels.Indel method)
get_mutation_sequences() (oncodrivefml.indels.Indel method)
get_ref() (in module oncodrivefml.reference)
get_ref_triplet() (in module oncodrivefml.reference)
get_score_by_position() (oncodrivefml.scores.Scores method)
get_stop_scores() (oncodrivefml.scores.Scores method)
gmean() (in module oncodrivefml.compute)
gmean_weighted() (in module oncodrivefml.compute)
GroupSignature (class in oncodrivefml.executors.sig2probs)
I
Indel (class in oncodrivefml.indels)
init_indels_module() (in module oncodrivefml.indels)
init_scores_module() (in module oncodrivefml.scores)
is_frameshift() (oncodrivefml.indels.Indel static method)
is_in_repetitive_region() (oncodrivefml.indels.Indel method)
is_valid_trinucleotides() (in module oncodrivefml.reference)
L
load() (in module oncodrivefml.signature)
load_configuration() (in module oncodrivefml.config)
loop_logging() (in module oncodrivefml.utils)
M
Maximum (class in oncodrivefml.stats)
mean() (oncodrivefml.indels.StopsScore method)
median() (oncodrivefml.indels.StopsScore method)
multiple_test_correction() (in module oncodrivefml.mtc)
mutations() (in module oncodrivefml.load)
mutations_and_elements() (in module oncodrivefml.load)
N
NoSignature (class in oncodrivefml.executors.sig2probs)
not_found() (oncodrivefml.indels.Indel method)
null() (in module oncodrivefml.scores)
O
oncodrivefml (module)
oncodrivefml.compute (module)
oncodrivefml.config (module)
oncodrivefml.error (module)
oncodrivefml.executors (module)
oncodrivefml.executors.sig2probs (module)
oncodrivefml.indels (module)
oncodrivefml.load (module)
oncodrivefml.mtc (module)
oncodrivefml.reference (module)
oncodrivefml.scores (module)
oncodrivefml.signature (module)
oncodrivefml.stats (module)
oncodrivefml.store (module)
oncodrivefml.utils (module)
OncodriveFMLError
P
PackScoresReader (class in oncodrivefml.scores)
possible_extensions (in module oncodrivefml.config)
probs (oncodrivefml.executors.sig2probs.GroupSignature attribute)
(oncodrivefml.executors.sig2probs.NoSignature attribute)
(oncodrivefml.executors.sig2probs.SubstitutionProbs attribute)
Q
QQPlot (class in oncodrivefml.store)
R
random() (oncodrivefml.indels.StopsScore method)
random_scores() (in module oncodrivefml.compute)
ReaderError
ReaderGetError
ref (oncodrivefml.scores.ScoreValue attribute)
ref_build (in module oncodrivefml.reference)
remove_extension_and_replace_special_characters() (in module oncodrivefml.config)
reverse_complementary_sequence() (in module oncodrivefml.reference)
S
SCORE_ALT (oncodrivefml.scores.PackScoresReader attribute)
SCORE_ORDER (oncodrivefml.scores.PackScoresReader attribute)
Scores (class in oncodrivefml.scores)
scores_by_pos (oncodrivefml.scores.Scores attribute)
ScoresTabixReader (class in oncodrivefml.scores)
ScoreValue (class in oncodrivefml.scores)
show() (oncodrivefml.store.QQPlot method)
size (oncodrivefml.executors.sig2probs.GroupSignature attribute)
(oncodrivefml.executors.sig2probs.NoSignature attribute)
(oncodrivefml.executors.sig2probs.SubstitutionProbs attribute)
snp() (in module oncodrivefml.load)
special_characters (in module oncodrivefml.config)
stop_function() (in module oncodrivefml.scores)
StopsScore (class in oncodrivefml.indels)
store_html() (in module oncodrivefml.store)
store_png() (in module oncodrivefml.store)
store_tsv() (in module oncodrivefml.store)
STRUCT_SIZE (oncodrivefml.scores.PackScoresReader attribute)
SubstitutionProbs (class in oncodrivefml.executors.sig2probs)
T
triplet_counter_executor() (in module oncodrivefml.reference)
triplets() (in module oncodrivefml.reference)
U
unpack() (oncodrivefml.scores.PackScoresReader method)
V
value (oncodrivefml.scores.ScoreValue attribute)
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