OncodriveFML
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OncodriveFML
OncodriveFML
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Configuration
Analysis
Signature
Output
Behind the scenes
Caveats
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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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 property)
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 property)
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)
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)
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)
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)
O
oncodrivefml (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 property)
(oncodrivefml.executors.sig2probs.NoSignature property)
(oncodrivefml.executors.sig2probs.SubstitutionProbs property)
Q
QQPlot (class in oncodrivefml.store)
R
random() (oncodrivefml.indels.StopsScore method)
ReaderError
ReaderGetError
ref() (oncodrivefml.scores.ScoreValue property)
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 property)
(oncodrivefml.executors.sig2probs.NoSignature property)
(oncodrivefml.executors.sig2probs.SubstitutionProbs property)
snp() (in module oncodrivefml.load)
special_characters (in module oncodrivefml.config)
stop_scores() (oncodrivefml.scores.Scores property)
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)
U
unpack() (oncodrivefml.scores.PackScoresReader method)
V
value() (oncodrivefml.scores.ScoreValue property)
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