CluBCpG
v0.1.22
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
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Index
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Symbols
--bin_size <bin_size>
clubcpg-cluster command line option
clubcpg-coverage command line option
clubcpg-impute-cluster command line option
--bins <bins>
clubcpg-cluster command line option
clubcpg-impute-cluster command line option
--chunksize <chunksize>
clubcpg-impute-cluster command line option
--models_A <models_a>
clubcpg-impute-cluster command line option
--models_B <models_b>
clubcpg-impute-cluster command line option
--no_overlap <no_overlap>
clubcpg-cluster command line option
clubcpg-coverage command line option
clubcpg-impute-cluster command line option
--permute <permute>
clubcpg-cluster command line option
--read1_3 <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 <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 <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 <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
--remove_noise <remove_noise>
clubcpg-cluster command line option
clubcpg-impute-cluster command line option
--suffix <suffix>
clubcpg-cluster command line option
clubcpg-impute-cluster command line option
-a <input_bam_a>, --input_bam_A <input_bam_a>
clubcpg-cluster command line option
clubcpg-coverage command line option
clubcpg-impute-cluster command line option
-a <input_bam_file>, --input_bam_file <input_bam_file>
clubcpg-impute-train command line option
clugcpg-impute-coverage command line option
-b <input_bam_b>, --input_bam_B <input_bam_b>
clubcpg-cluster command line option
clubcpg-impute-cluster command line option
-c <coverage>, --coverage <coverage>
clubcpg-impute-train command line option
clugcpg-impute-coverage command line option
-chr <chromosome>, --chromosome <chromosome>
clubcpg-coverage command line option
clugcpg-impute-coverage command line option
-h, --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
-l <limit_samples>, --limit_samples <limit_samples>
clubcpg-impute-train command line option
-m <cluster_member_minimum>, --cluster_member_minimum <cluster_member_minimum>
clubcpg-cluster command line option
clubcpg-impute-cluster command line option
-m <models>, --models <models>
clugcpg-impute-coverage command line option
-n <n>
clubcpg-impute-train command line option
clugcpg-impute-coverage command line option
-n <num_processors>, --num_processors <num_processors>
clubcpg-cluster command line option
clubcpg-coverage command line option
clubcpg-impute-cluster command line option
-o <output>, --output <output>
clubcpg-impute-train command line option
clugcpg-impute-coverage command line option
-o <output_dir>, --output_dir <output_dir>
clubcpg-cluster command line option
clubcpg-coverage command line option
clubcpg-impute-cluster command line option
-r <read_depth>, --read_depth <read_depth>
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 <bin_size>
--bins <bins>
--no_overlap <no_overlap>
--permute <permute>
--read1_3 <read1_3>
--read1_5 <read1_5>
--read2_3 <read2_3>
--read2_5 <read2_5>
--remove_noise <remove_noise>
--suffix <suffix>
-a <input_bam_a>, --input_bam_A <input_bam_a>
-b <input_bam_b>, --input_bam_B <input_bam_b>
-h, --help
-m <cluster_member_minimum>, --cluster_member_minimum <cluster_member_minimum>
-n <num_processors>, --num_processors <num_processors>
-o <output_dir>, --output_dir <output_dir>
-r <read_depth>, --read_depth <read_depth>
clubcpg-coverage command line option
--bin_size <bin_size>
--no_overlap <no_overlap>
--read1_3 <read1_3>
--read1_5 <read1_5>
--read2_3 <read2_3>
--read2_5 <read2_5>
-a <input_bam_a>, --input_bam_A <input_bam_a>
-chr <chromosome>, --chromosome <chromosome>
-h, --help
-n <num_processors>, --num_processors <num_processors>
-o <output_dir>, --output_dir <output_dir>
clubcpg-impute-cluster command line option
--bin_size <bin_size>
--bins <bins>
--chunksize <chunksize>
--models_A <models_a>
--models_B <models_b>
--no_overlap <no_overlap>
--read1_3 <read1_3>
--read1_5 <read1_5>
--read2_3 <read2_3>
--read2_5 <read2_5>
--remove_noise <remove_noise>
--suffix <suffix>
-a <input_bam_a>, --input_bam_A <input_bam_a>
-b <input_bam_b>, --input_bam_B <input_bam_b>
-h, --help
-m <cluster_member_minimum>, --cluster_member_minimum <cluster_member_minimum>
-n <num_processors>, --num_processors <num_processors>
-o <output_dir>, --output_dir <output_dir>
-r <read_depth>, --read_depth <read_depth>
clubcpg-impute-train command line option
--read1_3 <read1_3>
--read1_5 <read1_5>
--read2_3 <read2_3>
--read2_5 <read2_5>
-a <input_bam_file>, --input_bam_file <input_bam_file>
-c <coverage>, --coverage <coverage>
-h, --help
-l <limit_samples>, --limit_samples <limit_samples>
-n <n>
-o <output>, --output <output>
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
--read1_3 <read1_3>
--read1_5 <read1_5>
--read2_3 <read2_3>
--read2_5 <read2_5>
-a <input_bam_file>, --input_bam_file <input_bam_file>
-c <coverage>, --coverage <coverage>
-chr <chromosome>, --chromosome <chromosome>
-h, --help
-m <models>, --models <models>
-n <n>
-o <output>, --output <output>
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)
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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v: v0.1.22
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0.1.18
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