OncodriveFML
2.0.4
OncodriveFML
OncodriveFML
How it works
Files
Configuration
Analysis
Signature
Output
Behind the scenes
Caveats
Code documentation
oncodrivefml
OncodriveFML
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Index
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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
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Y
A
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)
alt_triplet (oncodrivefml.scores.ScoreValue attribute)
ArithmeticMean (class in oncodrivefml.stats)
ArithmeticMeanHeteroscedasticScores (class in oncodrivefml.stats)
B
BIT_TO_REF (oncodrivefml.scores.PackScoresReader attribute)
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_ref_build() (in module oncodrivefml.signature)
choose() (oncodrivefml.indels.StopsScore method)
chunkizator() (in module oncodrivefml.signature)
collapse_complementaries() (in module oncodrivefml.signature)
complementary_sequence() (in module oncodrivefml.signature)
compute_regions_signature() (in module oncodrivefml.signature)
compute_scores() (oncodrivefml.indels.Indel method)
compute_signature() (in module oncodrivefml.signature)
correct_signature_by_triplets_frequencies() (in module oncodrivefml.signature)
count_valid_trinucleotides() (in module oncodrivefml.signature)
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_alternate_signature() (in module oncodrivefml.signature)
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.signature)
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_normalized_frequencies() (in module oncodrivefml.signature)
get_ref() (in module oncodrivefml.signature)
get_ref_triplet() (in module oncodrivefml.signature)
get_reference_signature() (in module oncodrivefml.signature)
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)
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.signature)
L
load_and_map_variants() (in module oncodrivefml.load)
load_configuration() (in module oncodrivefml.config)
load_mutations() (in module oncodrivefml.load)
load_signature() (in module oncodrivefml.signature)
load_trinucleotides_counts() (in module oncodrivefml.signature)
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)
N
not_found() (oncodrivefml.indels.Indel method)
null() (in module oncodrivefml.scores)
O
oncodrivefml (module)
oncodrivefml.compute (module)
oncodrivefml.config (module)
oncodrivefml.executors (module)
oncodrivefml.indels (module)
oncodrivefml.load (module)
oncodrivefml.mtc (module)
oncodrivefml.scores (module)
oncodrivefml.signature (module)
oncodrivefml.stats (module)
oncodrivefml.store (module)
oncodrivefml.utils (module)
P
PackScoresReader (class in oncodrivefml.scores)
possible_extensions (in module oncodrivefml.config)
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.signature)
ref_triplet (oncodrivefml.scores.ScoreValue attribute)
remove_extension_and_replace_special_characters() (in module oncodrivefml.config)
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)
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)
sum2one_dict() (in module oncodrivefml.signature)
T
triplet_counter_executor() (in module oncodrivefml.signature)
triplets() (in module oncodrivefml.signature)
U
unpack() (oncodrivefml.scores.PackScoresReader method)
V
value (oncodrivefml.scores.ScoreValue attribute)
Y
yield_mutations() (in module oncodrivefml.signature)
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v: 2.0.4
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