AntPack
Installation and licensing
AntPack command line, Python and GUI tools
Using the GUI: a tutorial
How antibody numbering in AntPack works
Antibody numbering
Using DNA sequences
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
Clustering tutorial
Clustering example
About / Contact
AntPack
Index
Index
_
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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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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.LiabilitySearchTool attribute)
__init__() (antpack.DNASeqTranslator method)
(antpack.EMCategoricalMixture method)
(antpack.PairedChainAnnotator method)
(antpack.SingleChainAnnotator method)
,
[1]
(antpack.VJGeneTool method)
A
AIC() (antpack.EMCategoricalMixture method)
analyze_seq (antpack.LiabilitySearchTool attribute)
(antpack.PairedChainAnnotator attribute)
(antpack.SingleChainAnnotator attribute)
analyze_seqs (antpack.PairedChainAnnotator attribute)
(antpack.SingleChainAnnotator attribute)
assign_cdr_labels (antpack.PairedChainAnnotator attribute)
(antpack.SingleChainAnnotator attribute)
assign_vj_genes (antpack.VJGeneTool attribute)
B
BIC() (antpack.EMCategoricalMixture method)
build_distance_matrix (antpack.SingleChainAnnotator attribute)
build_msa (antpack.PairedChainAnnotator attribute)
(antpack.SingleChainAnnotator attribute)
C
calc_per_aa_probs() (antpack.SequenceScoringTool method)
convert_sequence_to_array() (antpack.SequenceScoringTool method)
D
DNASeqTranslator (class in antpack)
E
EMCategoricalMixture (class in antpack)
encode_fasta() (antpack.EMCategoricalMixture method)
F
fit() (antpack.EMCategoricalMixture method)
G
get_diagnostic_info() (antpack.SequenceScoringTool method)
get_model_parameters() (antpack.EMCategoricalMixture method)
get_model_specs() (antpack.EMCategoricalMixture method)
get_standard_mask() (antpack.SequenceScoringTool method)
get_standard_positions() (antpack.SequenceScoringTool method)
get_vj_gene_sequence (antpack.VJGeneTool attribute)
L
LiabilitySearchTool (class in antpack)
load_params() (antpack.EMCategoricalMixture method)
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)
S
score() (antpack.EMCategoricalMixture method)
score_seqs() (antpack.SequenceScoringTool method)
,
[1]
SequenceScoringTool (class in antpack)
,
[1]
,
[2]
SingleChainAnnotator (class in antpack)
,
[1]
sort_position_codes (antpack.PairedChainAnnotator attribute)
(antpack.SingleChainAnnotator attribute)
suggest_humanizing_mutations() (antpack.SequenceScoringTool method)
T
translate_dna_known_rf (antpack.DNASeqTranslator attribute)
translate_dna_unknown_rf (antpack.DNASeqTranslator attribute)
trim_alignment (antpack.PairedChainAnnotator attribute)
(antpack.SingleChainAnnotator attribute)
V
VJGeneTool (class in antpack)