metator
Contents:
tutorial
manual curation of metator mags
mags visualization and scaffolding
reference api
Contents:
tutorial
manual curation of metator mags
mags visualization and scaffolding
reference api
Quick search
Contents:
tutorial
Tutorial MetaTOR
manual curation of metator mags
Manual curation of the contaminated MetaTOR MAGs with anvio
mags visualization and scaffolding
MAG visualization and scaffolding
reference api
metator package
Docs
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Index
Index
A
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B
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C
|
D
|
E
|
F
|
G
|
L
|
M
|
N
|
P
|
Q
|
R
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S
|
U
|
V
|
W
A
AbstractCommand (class in metator.commands)
algo_partition() (in module metator.partition)
align() (in module metator.align)
alignment_to_contacts() (in module metator.network)
B
build_clustering_matrix() (in module metator.partition)
build_matrix_network() (in module metator.figures)
C
check_checkm() (in module metator.io)
check_fasta_index() (in module metator.io)
check_is_fasta() (in module metator.io)
check_louvain_cpp() (in module metator.io)
check_output_path() (metator.commands.AbstractCommand method)
check_pairix() (in module metator.io)
check_pairtools() (in module metator.io)
checkm() (in module metator.validation)
checkm_compare_bins() (in module metator.validation)
compute_network() (in module metator.network)
Contactmap (class in metator.commands)
correct_final_bin() (in module metator.validation)
create_contig_data() (in module metator.network)
D
defined_overlapping_bins() (in module metator.partition)
detect_core_bins() (in module metator.partition)
E
execute() (metator.commands.AbstractCommand method)
(metator.commands.Contactmap method)
(metator.commands.Network method)
(metator.commands.Pairs method)
(metator.commands.Partition method)
(metator.commands.Pipeline method)
(metator.commands.Qc method)
(metator.commands.Scaffold method)
(metator.commands.Validation method)
extract_pairs() (in module metator.contact_map)
F
figure_camembert_quality() (in module metator.figures)
figures_bins_distribution() (in module metator.figures)
figures_bins_size_distribution() (in module metator.figures)
figures_mags_GC_boxplots() (in module metator.figures)
figures_mags_HiC_cov_boxplots() (in module metator.figures)
figures_mags_SG_cov_boxplots() (in module metator.figures)
G
generate_contact_map() (in module metator.contact_map)
generate_fasta() (in module metator.partition)
generate_fasta_index() (in module metator.io)
generate_log_footer() (in module metator.commands)
generate_log_header() (in module metator.commands)
generate_temp_dir() (in module metator.io)
generates_frags_network() (in module metator.figures)
get_bin_coverage() (in module metator.validation)
get_contact_pairs() (in module metator.align)
get_contigs_data() (metator.contact_map.MetatorObject method)
get_distances_splitmat() (in module metator.partition)
get_hamming_distance() (in module metator.partition)
get_pairs_data() (in module metator.io)
get_restriction_site() (in module metator.io)
getrandbits() (in module metator.io)
give_results_info() (in module metator.validation)
L
leiden_iterations_java() (in module metator.partition)
louvain_iterations_cpp() (in module metator.partition)
M
main() (in module metator.main)
merge_alignment() (in module metator.align)
merge_micomplete() (in module metator.validation)
metator
module
metator.align
module
metator.commands
module
metator.contact_map
module
metator.figures
module
metator.io
module
metator.log
module
metator.main
module
metator.network
module
metator.partition
module
metator.validation
module
metator.version
module
MetatorObject (class in metator.contact_map)
micomplete_compare_bins() (in module metator.validation)
micomplete_quality() (in module metator.validation)
micomplete_results_to_dict() (in module metator.io)
module
metator
metator.align
metator.commands
metator.contact_map
metator.figures
metator.io
metator.log
metator.main
metator.network
metator.partition
metator.validation
metator.version
N
Network (class in metator.commands)
network_heatmap() (in module metator.figures)
normalize_pair() (in module metator.network)
P
Pairs (class in metator.commands)
Partition (class in metator.commands)
partition() (in module metator.partition)
Pipeline (class in metator.commands)
plot_figures() (in module metator.figures)
precompute_network() (in module metator.network)
process_bamfile() (in module metator.align)
process_bwa_bamfile() (in module metator.align)
Q
Qc (class in metator.commands)
R
read_bin_summary() (in module metator.io)
read_compressed() (in module metator.io)
read_contig_data() (in module metator.io)
read_results_checkm() (in module metator.io)
recursive_clustering() (in module metator.validation)
recursive_clustering_worker() (in module metator.validation)
recursive_decontamination() (in module metator.validation)
reindex_df() (in module metator.figures)
remove_isolates() (in module metator.partition)
retrieve_fasta() (in module metator.io)
S
save_sparse_matrix() (in module metator.io)
Scaffold (class in metator.commands)
set_contigs() (metator.contact_map.MetatorObject method)
set_file_handler() (in module metator.log)
set_large_contigs() (metator.contact_map.MetatorObject method)
set_metator_object() (metator.contact_map.MetatorObject method)
setup_text_logging() (in module metator.log)
sort_pairs() (in module metator.io)
sort_pairs_pairtools() (in module metator.io)
spinglass_partition() (in module metator.partition)
U
update_contigs_data() (in module metator.partition)
update_contigs_data_recursive() (in module metator.validation)
V
Validation (class in metator.commands)
W
write_bin_summary() (in module metator.io)
write_bins_contigs() (in module metator.validation)
write_contig_data() (in module metator.network)
write_fasta() (metator.contact_map.MetatorObject method)
write_hit_data() (in module metator.network)