CluBCpG
latest
User Guide Contents:
1. Getting Started
2. Using CluBCpG
3. Understanding the CluBCpG output data
4. Using CluBCpG with PReLIM
Developer Reference:
API documentation
CluBCpG
Index
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Index
Symbols
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A
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B
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C
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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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P
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R
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S
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T
Symbols
--bin_size
clubcpg-cluster command line option
clubcpg-coverage command line option
clubcpg-impute-cluster command line option
--bins
clubcpg-cluster command line option
clubcpg-impute-cluster command line option
--chromosome
clubcpg-coverage command line option
clugcpg-impute-coverage command line option
--chunksize
clubcpg-impute-cluster command line option
--cluster_member_minimum
clubcpg-cluster command line option
clubcpg-impute-cluster command line option
--coverage
clubcpg-impute-train command line option
clugcpg-impute-coverage command line option
--help
clubcpg-cluster command line option
clubcpg-coverage command line option
clubcpg-impute-cluster command line option
clubcpg-impute-train command line option
clugcpg-impute-coverage command line option
--input_bam_A
clubcpg-cluster command line option
clubcpg-coverage command line option
clubcpg-impute-cluster command line option
--input_bam_B
clubcpg-cluster command line option
clubcpg-impute-cluster command line option
--input_bam_file
clubcpg-impute-train command line option
clugcpg-impute-coverage command line option
--limit_samples
clubcpg-impute-train command line option
--models
clugcpg-impute-coverage command line option
--models_A
clubcpg-impute-cluster command line option
--models_B
clubcpg-impute-cluster command line option
--no_overlap
clubcpg-cluster command line option
clubcpg-coverage command line option
clubcpg-impute-cluster command line option
--num_processors
clubcpg-cluster command line option
clubcpg-coverage command line option
clubcpg-impute-cluster command line option
--output
clubcpg-impute-train command line option
clugcpg-impute-coverage command line option
--output_dir
clubcpg-cluster command line option
clubcpg-coverage command line option
clubcpg-impute-cluster command line option
--permute
clubcpg-cluster command line option
--read1_3
clubcpg-cluster command line option
clubcpg-coverage command line option
clubcpg-impute-cluster command line option
clubcpg-impute-train command line option
clugcpg-impute-coverage command line option
--read1_5
clubcpg-cluster command line option
clubcpg-coverage command line option
clubcpg-impute-cluster command line option
clubcpg-impute-train command line option
clugcpg-impute-coverage command line option
--read2_3
clubcpg-cluster command line option
clubcpg-coverage command line option
clubcpg-impute-cluster command line option
clubcpg-impute-train command line option
clugcpg-impute-coverage command line option
--read2_5
clubcpg-cluster command line option
clubcpg-coverage command line option
clubcpg-impute-cluster command line option
clubcpg-impute-train command line option
clugcpg-impute-coverage command line option
--read_depth
clubcpg-cluster command line option
clubcpg-impute-cluster command line option
--remove_noise
clubcpg-cluster command line option
clubcpg-impute-cluster command line option
--suffix
clubcpg-cluster command line option
clubcpg-impute-cluster command line option
-a
clubcpg-cluster command line option
clubcpg-coverage command line option
clubcpg-impute-cluster command line option
clubcpg-impute-train command line option
clugcpg-impute-coverage command line option
-b
clubcpg-cluster command line option
clubcpg-impute-cluster command line option
-c
clubcpg-impute-train command line option
clugcpg-impute-coverage command line option
-chr
clubcpg-coverage command line option
clugcpg-impute-coverage command line option
-h
clubcpg-cluster command line option
clubcpg-coverage command line option
clubcpg-impute-cluster command line option
clubcpg-impute-train command line option
clugcpg-impute-coverage command line option
-l
clubcpg-impute-train command line option
-m
clubcpg-cluster command line option
clubcpg-impute-cluster command line option
clugcpg-impute-coverage command line option
-n
clubcpg-cluster command line option
clubcpg-coverage command line option
clubcpg-impute-cluster command line option
clubcpg-impute-train command line option
clugcpg-impute-coverage command line option
-o
clubcpg-cluster command line option
clubcpg-coverage command line option
clubcpg-impute-cluster command line option
clubcpg-impute-train command line option
clugcpg-impute-coverage command line option
-r
clubcpg-cluster command line option
clubcpg-impute-cluster command line option
_
__init__() (clubcpg.CalculateBinCoverage.CalculateCompleteBins method)
(clubcpg.ClusterReads.ClusterReads method)
(clubcpg.ClusterReads.ClusterReadsWithImputation method)
(clubcpg.ConnectToCpGNet.TrainWithPReLIM method)
(clubcpg.Imputation.Imputation method)
(clubcpg.ParseBam.BamFileReadParser method)
(clubcpg_prelim.PReLIM.CpGBin method)
(clubcpg_prelim.PReLIM.PReLIM method)
A
analyze_bins() (clubcpg.CalculateBinCoverage.CalculateCompleteBins method)
attempt_cpg_position_correction() (clubcpg.ClusterReads.ClusterReads static method)
B
BamFileReadParser (class in clubcpg.ParseBam)
C
calculate_bin_coverage() (clubcpg.CalculateBinCoverage.CalculateCompleteBins method)
CalculateCompleteBins (class in clubcpg.CalculateBinCoverage)
clubcpg-cluster command line option
--bin_size
--bins
--cluster_member_minimum
--help
--input_bam_A
--input_bam_B
--no_overlap
--num_processors
--output_dir
--permute
--read1_3
--read1_5
--read2_3
--read2_5
--read_depth
--remove_noise
--suffix
-a
-b
-h
-m
-n
-o
-r
clubcpg-coverage command line option
--bin_size
--chromosome
--help
--input_bam_A
--no_overlap
--num_processors
--output_dir
--read1_3
--read1_5
--read2_3
--read2_5
-a
-chr
-h
-n
-o
clubcpg-impute-cluster command line option
--bin_size
--bins
--chunksize
--cluster_member_minimum
--help
--input_bam_A
--input_bam_B
--models_A
--models_B
--no_overlap
--num_processors
--output_dir
--read1_3
--read1_5
--read2_3
--read2_5
--read_depth
--remove_noise
--suffix
-a
-b
-h
-m
-n
-o
-r
clubcpg-impute-train command line option
--coverage
--help
--input_bam_file
--limit_samples
--output
--read1_3
--read1_5
--read2_3
--read2_5
-a
-c
-h
-l
-n
-o
clubcpg.CalculateBinCoverage
module
clubcpg.ClusterReads
module
clubcpg.ConnectToCpGNet
module
clubcpg.Imputation
module
clubcpg.ParseBam
module
clubcpg_prelim.PReLIM
module
clugcpg-impute-coverage command line option
--chromosome
--coverage
--help
--input_bam_file
--models
--output
--read1_3
--read1_5
--read2_3
--read2_5
-a
-c
-chr
-h
-m
-n
-o
ClusterReads (class in clubcpg.ClusterReads)
ClusterReadsWithImputation (class in clubcpg.ClusterReads)
correct_cpg_positions() (clubcpg.ParseBam.BamFileReadParser static method)
CpGBin (class in clubcpg_prelim.PReLIM)
create_matrix() (clubcpg.ParseBam.BamFileReadParser method)
E
execute() (clubcpg.ClusterReads.ClusterReads method)
(clubcpg.ClusterReads.ClusterReadsWithImputation method)
extract_matrices() (clubcpg.Imputation.Imputation method)
F
filter_data_frame() (clubcpg.ClusterReads.ClusterReads method)
fit() (clubcpg_prelim.PReLIM.PReLIM method)
fix_read_overlap() (clubcpg.ParseBam.BamFileReadParser method)
G
generate_bins_list() (clubcpg.CalculateBinCoverage.CalculateCompleteBins method)
generate_individual_matrix_data() (clubcpg.ClusterReads.ClusterReads method)
get_chromosome_lengths() (clubcpg.CalculateBinCoverage.CalculateCompleteBins method)
I
Imputation (class in clubcpg.Imputation)
impute() (clubcpg_prelim.PReLIM.PReLIM method)
impute_from_model() (clubcpg.Imputation.Imputation method)
impute_many() (clubcpg_prelim.PReLIM.PReLIM method)
L
loadWeights() (clubcpg_prelim.PReLIM.PReLIM method)
M
module
clubcpg.CalculateBinCoverage
clubcpg.ClusterReads
clubcpg.ConnectToCpGNet
clubcpg.Imputation
clubcpg.ParseBam
clubcpg_prelim.PReLIM
P
parse_reads() (clubcpg.ParseBam.BamFileReadParser method)
postprocess_predictions() (clubcpg.Imputation.Imputation static method)
predict() (clubcpg_prelim.PReLIM.PReLIM method)
predict_classes() (clubcpg_prelim.PReLIM.PReLIM method)
predict_proba() (clubcpg_prelim.PReLIM.PReLIM method)
PReLIM (class in clubcpg_prelim.PReLIM)
process_bins() (clubcpg.ClusterReads.ClusterReads method)
R
remove_scaffolds() (clubcpg.CalculateBinCoverage.CalculateCompleteBins static method)
S
save_net() (clubcpg.ConnectToCpGNet.TrainWithPReLIM method)
T
train() (clubcpg_prelim.PReLIM.PReLIM method)
train_model() (clubcpg.ConnectToCpGNet.TrainWithPReLIM method)
(clubcpg.Imputation.Imputation method)
TrainWithPReLIM (class in clubcpg.ConnectToCpGNet)
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