Aldy
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Contents:
Algorithm details
⚠️ Warning
Installation
Sanity check
Running
Output
Sample datasets
License
Parameters & Usage
Gene Support
Change log
Acknowledgments
Contact & Bug Reports
API Tutorial
Database Specification
API documentation
Aldy
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Index
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Index
A
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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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H
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I
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J
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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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W
A
abssum() (aldy.lpinterface.Gurobi method)
activity (aldy.gene.MinorAllele attribute)
addConstr() (aldy.lpinterface.CBC method)
(aldy.lpinterface.Gurobi method)
addVar() (aldy.lpinterface.CBC method)
(aldy.lpinterface.Gurobi method)
aldy.cn (module)
aldy.common (module)
aldy.coverage (module)
aldy.diplotype (module)
aldy.gene (module)
aldy.lpinterface (module)
aldy.major (module)
aldy.minor (module)
aldy.profile (module)
AldyException
allele_name() (in module aldy.common)
alleles (aldy.gene.Gene attribute)
alt_name (aldy.gene.MinorAllele attribute)
aminoacid (aldy.gene.Gene attribute)
average_coverage() (aldy.coverage.Coverage method)
B
basic_filter() (aldy.coverage.Coverage method)
C
CBC (class in aldy.lpinterface)
chr (aldy.gene.Gene attribute)
chr_prefix() (in module aldy.common)
chr_to_ref (aldy.gene.Gene attribute)
cn_config (aldy.gene.MajorAllele attribute)
cn_configs (aldy.gene.Gene attribute)
cn_diff (aldy.profile.Profile attribute)
cn_fit (aldy.profile.Profile attribute)
cn_fusion_left (aldy.profile.Profile attribute)
cn_fusion_right (aldy.profile.Profile attribute)
cn_max (aldy.profile.Profile attribute)
cn_parsimony (aldy.profile.Profile attribute)
cn_pce_penalty (aldy.profile.Profile attribute)
cn_region (aldy.profile.Profile attribute)
cn_solution (aldy.profile.Profile attribute)
CNConfig (class in aldy.gene)
CNConfigType (class in aldy.gene)
colorize() (in module aldy.common)
common_tandems (aldy.gene.Gene attribute)
Coverage (class in aldy.coverage)
coverage() (aldy.coverage.Coverage method)
D
data (aldy.profile.Profile attribute)
DEFAULT (aldy.gene.CNConfigType attribute)
DELETION (aldy.gene.CNConfigType attribute)
deletion_allele() (aldy.gene.Gene method)
description (aldy.gene.CNConfig attribute)
diploid_avg_coverage() (aldy.coverage.Coverage method)
display_format (aldy.profile.Profile attribute)
do_copy_number (aldy.gene.Gene attribute)
dump() (aldy.coverage.Coverage method)
(aldy.lpinterface.CBC method)
(aldy.lpinterface.Gurobi method)
E
ensembl (aldy.gene.Gene attribute)
escape_name() (in module aldy.lpinterface)
estimate_cn() (in module aldy.cn)
estimate_diplotype() (in module aldy.diplotype)
estimate_major() (in module aldy.major)
estimate_minor() (in module aldy.minor)
evidence (aldy.gene.MinorAllele attribute)
exons (aldy.gene.Gene attribute)
F
filtered() (aldy.coverage.Coverage method)
freezekey() (in module aldy.common)
G
gap (aldy.profile.Profile attribute)
Gene (class in aldy.gene)
genome (aldy.gene.Gene attribute)
get_allele() (aldy.gene.Gene method)
get_functional() (aldy.gene.Gene method)
get_minor_mutations() (aldy.gene.MajorAllele method)
get_refseq() (aldy.gene.Gene method)
get_rsid() (aldy.gene.Gene method)
get_sam_profile_data() (aldy.profile.Profile static method)
get_wide_region() (aldy.gene.Gene method)
getValue() (aldy.lpinterface.CBC method)
(aldy.lpinterface.Gurobi method)
GRange (class in aldy.common)
Gurobi (class in aldy.lpinterface)
H
has_coverage() (aldy.gene.Gene method)
I
is_binary() (aldy.lpinterface.CBC method)
(aldy.lpinterface.Gurobi method)
is_functional() (aldy.gene.Gene method)
J
JsonDict (class in aldy.common)
L
LEFT_FUSION (aldy.gene.CNConfigType attribute)
load() (aldy.profile.Profile static method)
log (in module aldy.common)
M
major_novel (aldy.profile.Profile attribute)
MajorAllele (class in aldy.gene)
male (aldy.profile.Profile attribute)
max_minor_solutions (aldy.profile.Profile attribute)
min_coverage (aldy.profile.Profile attribute)
min_mapq (aldy.profile.Profile attribute)
min_quality (aldy.profile.Profile attribute)
minor_add (aldy.profile.Profile attribute)
minor_miss (aldy.profile.Profile attribute)
minor_phase (aldy.profile.Profile attribute)
minor_phase_vars (aldy.profile.Profile attribute)
MinorAllele (class in aldy.gene)
model() (in module aldy.lpinterface)
Mutation (class in aldy.gene)
mutations (aldy.gene.Gene attribute)
N
name (aldy.gene.Gene attribute)
(aldy.profile.Profile attribute)
neutral_value (aldy.profile.Profile attribute)
NoSolutionsError
O
op (aldy.gene.Mutation attribute)
OUTPUT_COLS (in module aldy.diplotype)
P
parse_cn_region() (in module aldy.common)
percentage() (aldy.coverage.Coverage method)
pharmvar (aldy.gene.Gene attribute)
(aldy.gene.MinorAllele attribute)
phase (aldy.profile.Profile attribute)
pos (aldy.gene.Mutation attribute)
pp() (in module aldy.common)
prod() (aldy.lpinterface.Gurobi method)
Profile (class in aldy.profile)
PROTEINS (in module aldy.common)
pseudogenes (aldy.gene.Gene attribute)
Q
quality_filter() (aldy.coverage.Coverage method)
quicksum() (aldy.lpinterface.CBC method)
(aldy.lpinterface.Gurobi method)
R
random_mutations (aldy.gene.Gene attribute)
ref_to_chr (aldy.gene.Gene attribute)
refseq (aldy.gene.Gene attribute)
region_at() (aldy.gene.Gene method)
region_coverage() (aldy.coverage.Coverage method)
regions (aldy.gene.Gene attribute)
rev_comp() (in module aldy.common)
REV_COMPLEMENT (in module aldy.common)
RIGHT_FUSION (aldy.gene.CNConfigType attribute)
S
sam_long_reads (aldy.profile.Profile attribute)
sam_mappy_preset (aldy.profile.Profile attribute)
samtools() (aldy.common.GRange method)
script_path() (in module aldy.common)
seq (aldy.gene.Gene attribute)
seq_to_amino() (in module aldy.common)
setObjective() (aldy.lpinterface.CBC method)
(aldy.lpinterface.Gurobi method)
single_copy() (aldy.coverage.Coverage method)
SOLUTION_PRECISION (in module aldy.common)
solutions() (aldy.lpinterface.Gurobi method)
solve() (aldy.lpinterface.CBC method)
(aldy.lpinterface.Gurobi method)
solve_cn_model() (in module aldy.cn)
solve_major_model() (in module aldy.major)
solve_minor_model() (in module aldy.minor)
SOLVER_PRECISON (in module aldy.lpinterface)
sorted_tuple() (in module aldy.common)
strand (aldy.gene.Gene attribute)
T
td() (in module aldy.common)
threshold (aldy.profile.Profile attribute)
Timing (class in aldy.common)
total() (aldy.coverage.Coverage method)
U
unique_regions (aldy.gene.Gene attribute)
update() (aldy.lpinterface.CBC method)
(aldy.lpinterface.Gurobi method)
(aldy.profile.Profile method)
V
variables() (aldy.lpinterface.CBC method)
(aldy.lpinterface.Gurobi method)
varName() (aldy.lpinterface.CBC method)
(aldy.lpinterface.Gurobi method)
version (aldy.gene.Gene attribute)
W
write_decomposition() (in module aldy.diplotype)
write_vcf() (in module aldy.diplotype)
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