AntPack
Installation and licensing
AntPack command line, Python and GUI tools
Using the GUI: a tutorial
How antibody numbering in AntPack works
Antibody numbering
Numbering example
VJ gene assignment tutorial
VJ gene assignment example
Finding liabilities
How humanness evaluation in AntPack works
Scoring sequences for humanness in AntPack
Humanizing sequences with AntPack
Scoring and identifying problematic residues/motifs examples
Generating new human sequences
Search & clustering overview
Database search and clustering tutorial
Clustering for small datasets and frameworks
Some examples of clustering
About / Contact
AntPack
Index
Index
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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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L
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P
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R
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S
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T
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V
_
__init__() (antpack.EMCategoricalMixture method)
(antpack.LiabilitySearchTool method)
(antpack.LocalDBSearchTool method)
(antpack.PairedChainAnnotator method)
(antpack.SingleChainAnnotator method)
,
[1]
(antpack.VJGeneTool method)
A
AIC() (antpack.EMCategoricalMixture method)
analyze_seq() (antpack.LiabilitySearchTool method)
(antpack.PairedChainAnnotator method)
(antpack.SingleChainAnnotator method)
analyze_seqs() (antpack.PairedChainAnnotator method)
(antpack.SingleChainAnnotator method)
assign_cdr_labels() (antpack.PairedChainAnnotator method)
(antpack.SingleChainAnnotator method)
assign_vj_genes() (antpack.VJGeneTool method)
B
basic_clustering() (antpack.LocalDBSearchTool method)
BIC() (antpack.EMCategoricalMixture method)
build_database_from_cdr_only_csv() (in module antpack)
build_database_from_fasta() (in module antpack)
build_database_from_full_chain_csv() (in module antpack)
build_distance_matrix() (antpack.SingleChainAnnotator method)
build_msa() (antpack.PairedChainAnnotator method)
(antpack.SingleChainAnnotator method)
C
calc_per_aa_probs() (antpack.SequenceScoringTool method)
convert_sequence_to_array() (antpack.SequenceScoringTool method)
E
EMCategoricalMixture (class in antpack)
encode_fasta() (antpack.EMCategoricalMixture method)
F
fit() (antpack.EMCategoricalMixture method)
G
get_database_metadata() (antpack.LocalDBSearchTool method)
get_diagnostic_info() (antpack.SequenceScoringTool method)
get_max_seqid() (antpack.LocalDBSearchTool method)
get_model_parameters() (antpack.EMCategoricalMixture method)
get_model_specs() (antpack.EMCategoricalMixture method)
get_num_seqs() (antpack.LocalDBSearchTool method)
get_sequence() (antpack.LocalDBSearchTool method)
get_standard_mask() (antpack.SequenceScoringTool method)
get_standard_positions() (antpack.SequenceScoringTool method)
get_vgene_jgene() (antpack.LocalDBSearchTool method)
get_vj_gene_sequence() (antpack.VJGeneTool method)
L
LiabilitySearchTool (class in antpack)
load_params() (antpack.EMCategoricalMixture method)
LocalDBSearchTool (class in antpack)
P
PairedChainAnnotator (class in antpack)
predict() (antpack.EMCategoricalMixture method)
predict_proba() (antpack.EMCategoricalMixture method)
R
retrieve_cluster() (antpack.SequenceScoringTool method)
,
[1]
retrieve_db_dates() (antpack.VJGeneTool method)
retrieve_preprocessed_search_data() (antpack.LocalDBSearchTool method)
S
score() (antpack.EMCategoricalMixture method)
score_seqs() (antpack.SequenceScoringTool method)
,
[1]
search() (antpack.LocalDBSearchTool method)
search_from_preprocessed_data() (antpack.LocalDBSearchTool method)
SequenceScoringTool (class in antpack)
,
[1]
,
[2]
SingleChainAnnotator (class in antpack)
,
[1]
sort_position_codes() (antpack.PairedChainAnnotator method)
(antpack.SingleChainAnnotator method)
suggest_humanizing_mutations() (antpack.SequenceScoringTool method)
T
trim_alignment() (antpack.PairedChainAnnotator method)
(antpack.SingleChainAnnotator method)
V
VJGeneTool (class in antpack)