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epitopepredict
epitopepredict
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W
A
add_dicts() (in module epitopepredict.utilities)
aggregate_summary() (in module epitopepredict.web)
align_blast_results() (in module epitopepredict.analysis)
alignment_to_dataframe() (in module epitopepredict.analysis)
(in module epitopepredict.sequtils)
allele_mapping() (epitopepredict.base.NetMHCIIPanPredictor method)
allele_summary() (epitopepredict.base.Predictor method)
allelenumber() (in module epitopepredict.tepitope)
anchor_mutated() (in module epitopepredict.neo)
B
BasicMHCIPredictor (class in epitopepredict.base)
benchmark() (in module epitopepredict.tepitope)
binders_to_coords() (in module epitopepredict.plotting)
blast_sequences() (in module epitopepredict.sequtils)
bokeh_pie_chart() (in module epitopepredict.plotting)
bokeh_plot_bar() (in module epitopepredict.plotting)
bokeh_plot_grid() (in module epitopepredict.plotting)
bokeh_plot_sequence() (in module epitopepredict.plotting)
bokeh_plot_tracks() (in module epitopepredict.plotting)
bokeh_summary_plot() (in module epitopepredict.plotting)
bokeh_test() (in module epitopepredict.plotting)
bokeh_vbar() (in module epitopepredict.plotting)
C
check_alleles() (epitopepredict.base.Predictor method)
(epitopepredict.base.TEpitopePredictor method)
check_ensembl() (in module epitopepredict.neo)
check_imports() (in module epitopepredict.neo)
check_install() (epitopepredict.base.BasicMHCIPredictor method)
(epitopepredict.base.IEDBMHCIIPredictor method)
(epitopepredict.base.IEDBMHCIPredictor method)
(epitopepredict.base.MHCFlurryPredictor method)
(epitopepredict.base.NetMHCIIPanPredictor method)
(epitopepredict.base.NetMHCPanPredictor method)
(epitopepredict.base.Predictor method)
check_options() (in module epitopepredict.config)
check_snap() (in module epitopepredict.base)
check_tags() (in module epitopepredict.sequtils)
clean_sequence() (in module epitopepredict.base)
cleanup() (epitopepredict.base.Predictor method)
clustal_alignment() (in module epitopepredict.sequtils)
column_to_url() (in module epitopepredict.web)
combine_samples() (epitopepredict.neo.NeoEpitopeWorkFlow method)
combine_wt_scores() (in module epitopepredict.neo)
compare() (in module epitopepredict.tepitope)
compare_alleles() (in module epitopepredict.tepitope)
compare_anchor_positions() (in module epitopepredict.peptutils)
compare_predictors() (in module epitopepredict.base)
compare_ref() (in module epitopepredict.tepitope)
compare_tepitope_alleles() (in module epitopepredict.tepitope)
compress() (in module epitopepredict.utilities)
convert_allele_name() (epitopepredict.base.MHCFlurryPredictor method)
(epitopepredict.base.NetMHCIIPanPredictor method)
(epitopepredict.base.NetMHCPanPredictor method)
convert_allele_names() (in module epitopepredict.tepitope)
convert_sequence_format() (in module epitopepredict.sequtils)
copyfile() (in module epitopepredict.utilities)
copyfiles() (in module epitopepredict.utilities)
create_bokeh_table() (in module epitopepredict.web)
create_config_parser_from_dict() (in module epitopepredict.config)
create_figures() (in module epitopepredict.web)
create_fragments() (in module epitopepredict.peptutils)
create_nmers() (in module epitopepredict.analysis)
create_random_peptides() (in module epitopepredict.peptutils)
create_random_sequences() (in module epitopepredict.peptutils)
create_sequence_html() (in module epitopepredict.web)
create_virtual_pssm() (in module epitopepredict.tepitope)
create_widgets() (in module epitopepredict.web)
D
dataframe_to_fasta() (in module epitopepredict.sequtils)
dataframe_to_seqrecords() (in module epitopepredict.sequtils)
dataframe_to_vcf() (in module epitopepredict.neo)
DataFrameIterator (class in epitopepredict.base)
dataframes_to_html() (in module epitopepredict.web)
dbscan() (in module epitopepredict.analysis)
dict_to_html() (in module epitopepredict.web)
distance_tree() (in module epitopepredict.sequtils)
draw_genome_map() (in module epitopepredict.sequtils)
draw_labels() (in module epitopepredict.plotting)
DummyPredictor (class in epitopepredict.base)
E
effects_to_dataframe() (in module epitopepredict.neo)
effects_to_pickle() (in module epitopepredict.neo)
embl_to_dataframe() (in module epitopepredict.sequtils)
epitope_conservation() (in module epitopepredict.analysis)
epitopepredict (module)
epitopepredict.analysis (module)
epitopepredict.base (module)
epitopepredict.config (module)
epitopepredict.neo (module)
epitopepredict.peptutils (module)
epitopepredict.plotting (module)
epitopepredict.sequtils (module)
epitopepredict.tepitope (module)
epitopepredict.tests (module)
epitopepredict.utilities (module)
epitopepredict.web (module)
ete_tree() (in module epitopepredict.sequtils)
evaluate() (epitopepredict.base.Predictor method)
F
fasta_format_from_feature() (in module epitopepredict.sequtils)
fasta_to_dataframe() (in module epitopepredict.sequtils)
features_summary() (in module epitopepredict.sequtils)
features_to_dataframe() (in module epitopepredict.sequtils)
fetch_ensembl_release() (in module epitopepredict.neo)
fetch_protein_sequences() (in module epitopepredict.sequtils)
filter_iedb_file() (in module epitopepredict.utilities)
find_clusters() (in module epitopepredict.analysis)
find_conserved_peptide() (in module epitopepredict.analysis)
find_conserved_sequences() (in module epitopepredict.analysis)
find_filefrom_string() (in module epitopepredict.utilities)
find_files() (in module epitopepredict.utilities)
find_folders() (in module epitopepredict.utilities)
find_keyword() (in module epitopepredict.sequtils)
find_matches() (in module epitopepredict.neo)
first() (in module epitopepredict.base)
format_alignment() (in module epitopepredict.sequtils)
format_row() (epitopepredict.base.Predictor method)
G
genbank_to_dataframe() (in module epitopepredict.sequtils)
generate_pssm() (in module epitopepredict.tepitope)
get_AAcontent() (in module epitopepredict.analysis)
get_AAfraction() (in module epitopepredict.peptutils)
get_AAsubstitutions() (in module epitopepredict.peptutils)
get_all_fragments() (in module epitopepredict.peptutils)
get_allele_cutoffs() (epitopepredict.base.Predictor method)
get_allele_data() (epitopepredict.base.IEDBMHCIPredictor method)
get_allele_pocket_sequences() (in module epitopepredict.tepitope)
get_alleles() (epitopepredict.base.BasicMHCIPredictor method)
(epitopepredict.base.IEDBMHCIIPredictor method)
(epitopepredict.base.IEDBMHCIPredictor method)
(epitopepredict.base.MHCFlurryPredictor method)
(epitopepredict.base.NetMHCIIPanPredictor method)
(epitopepredict.base.NetMHCPanPredictor method)
(epitopepredict.base.Predictor method)
(epitopepredict.base.TEpitopePredictor method)
(in module epitopepredict.neo)
(in module epitopepredict.tepitope)
(in module epitopepredict.web)
get_binders() (epitopepredict.base.Predictor method)
get_blast_results() (in module epitopepredict.sequtils)
get_bokeh_colors() (in module epitopepredict.plotting)
get_cds() (in module epitopepredict.sequtils)
get_closest_match() (in module epitopepredict.neo)
get_closest_matches() (in module epitopepredict.neo)
get_coords() (in module epitopepredict.base)
get_dqp_list() (in module epitopepredict.base)
get_drb_list() (in module epitopepredict.base)
get_feature_qualifier() (in module epitopepredict.sequtils)
get_file_labels() (epitopepredict.neo.NeoEpitopeWorkFlow method)
get_file_lists() (in module epitopepredict.web)
get_filenames() (in module epitopepredict.base)
get_fragments() (in module epitopepredict.peptutils)
get_genes_by_location() (in module epitopepredict.sequtils)
get_global_rank() (epitopepredict.base.Predictor method)
get_identity() (in module epitopepredict.sequtils)
get_iedb_request() (in module epitopepredict.base)
get_length() (in module epitopepredict.base)
get_matrix() (in module epitopepredict.tepitope)
get_mutant_sequences() (in module epitopepredict.neo)
get_names() (epitopepredict.base.Predictor method)
get_nearest() (in module epitopepredict.base)
get_options() (in module epitopepredict.config)
get_orthologs() (in module epitopepredict.analysis)
get_overlapping() (in module epitopepredict.base)
get_overlaps() (in module epitopepredict.analysis)
get_pocket_positions() (in module epitopepredict.tepitope)
get_pockets_pseudo_sequence() (in module epitopepredict.tepitope)
get_pos() (in module epitopepredict.base)
get_predictor() (in module epitopepredict.base)
get_predictor_classes() (in module epitopepredict.base)
get_predictors() (in module epitopepredict.web)
get_preset_alleles() (in module epitopepredict.base)
get_pseudo_sequence() (in module epitopepredict.tepitope)
get_pssm_score() (in module epitopepredict.tepitope)
get_pssms() (in module epitopepredict.tepitope)
get_quantile_data() (epitopepredict.base.Predictor method)
get_quantiles() (in module epitopepredict.base)
get_ranking() (epitopepredict.base.Predictor method)
get_readme() (in module epitopepredict.web)
get_results_info() (in module epitopepredict.web)
get_results_tables() (in module epitopepredict.web)
get_scores() (epitopepredict.base.Predictor method)
(in module epitopepredict.tepitope)
get_scrollable_table() (in module epitopepredict.web)
get_seq_from_binders() (in module epitopepredict.plotting)
get_seqdepot() (in module epitopepredict.analysis)
get_seqdepot_annotation() (in module epitopepredict.plotting)
get_sequence() (in module epitopepredict.base)
(in module epitopepredict.sequtils)
get_sequence_colors() (in module epitopepredict.plotting)
get_sequencefrom_pdb() (in module epitopepredict.utilities)
get_sequences() (in module epitopepredict.web)
get_similarities() (in module epitopepredict.tepitope)
get_species_name() (in module epitopepredict.analysis)
get_standard_mhc1() (in module epitopepredict.base)
get_standard_mhc2() (in module epitopepredict.base)
get_summary_tables() (in module epitopepredict.web)
get_symmetric_data_frame() (in module epitopepredict.utilities)
get_translation() (in module epitopepredict.sequtils)
get_unique_cores() (epitopepredict.base.Predictor method)
get_variant_class() (in module epitopepredict.neo)
get_variants_effects() (in module epitopepredict.neo)
I
IEDBMHCIIPredictor (class in epitopepredict.base)
IEDBMHCIPredictor (class in epitopepredict.base)
index_genbank_features() (in module epitopepredict.sequtils)
isoelectric_point() (in module epitopepredict.analysis)
L
load() (epitopepredict.base.Predictor method)
load_variants() (in module epitopepredict.neo)
local_blast() (in module epitopepredict.sequtils)
M
main() (in module epitopepredict.peptutils)
(in module epitopepredict.tepitope)
make_blastdb() (in module epitopepredict.neo)
make_human_blastdb() (in module epitopepredict.neo)
make_virus_blastdb() (in module epitopepredict.neo)
MHCFlurryPredictor (class in epitopepredict.base)
muscle_alignment() (in module epitopepredict.sequtils)
N
needle_alignment() (in module epitopepredict.sequtils)
NeoEpitopeWorkFlow (class in epitopepredict.neo)
net_charge() (in module epitopepredict.analysis)
(in module epitopepredict.peptutils)
NetMHCIIPanPredictor (class in epitopepredict.base)
NetMHCPanPredictor (class in epitopepredict.base)
next() (epitopepredict.base.DataFrameIterator method)
P
pairwise_alignment() (in module epitopepredict.sequtils)
parse_config() (in module epitopepredict.config)
pbmec_score() (in module epitopepredict.neo)
peptide_properties() (in module epitopepredict.analysis)
peptides_from_effect() (in module epitopepredict.neo)
pickpocket() (in module epitopepredict.tepitope)
plot() (epitopepredict.base.Predictor method)
plot_bars() (in module epitopepredict.plotting)
plot_bcell() (in module epitopepredict.plotting)
plot_binder_map() (in module epitopepredict.plotting)
plot_heatmap() (in module epitopepredict.plotting)
plot_multiple() (in module epitopepredict.plotting)
plot_overview() (in module epitopepredict.plotting)
plot_regions() (in module epitopepredict.plotting)
plot_seqdepot() (in module epitopepredict.plotting)
plot_summary_heatmap() (in module epitopepredict.base)
plot_tracks() (in module epitopepredict.plotting)
plot_variant_summary() (in module epitopepredict.neo)
predict() (epitopepredict.base.BasicMHCIPredictor method)
(epitopepredict.base.DummyPredictor method)
(epitopepredict.base.IEDBMHCIIPredictor method)
(epitopepredict.base.IEDBMHCIPredictor method)
(epitopepredict.base.MHCFlurryPredictor method)
(epitopepredict.base.NetMHCIIPanPredictor method)
(epitopepredict.base.NetMHCPanPredictor method)
(epitopepredict.base.Predictor method)
(epitopepredict.base.TEpitopePredictor method)
predict_binding() (in module epitopepredict.neo)
predict_peptides() (epitopepredict.base.BasicMHCIPredictor method)
(epitopepredict.base.MHCFlurryPredictor method)
(epitopepredict.base.Predictor method)
predict_peptides_worker() (in module epitopepredict.base)
predict_proteins() (epitopepredict.base.Predictor method)
predict_proteins_worker() (in module epitopepredict.base)
predict_sequences() (epitopepredict.base.BasicMHCIPredictor method)
(epitopepredict.base.MHCFlurryPredictor method)
(epitopepredict.base.Predictor method)
prediction_coverage() (in module epitopepredict.analysis)
Predictor (class in epitopepredict.base)
PredictorTests (class in epitopepredict.tests)
prepare_data() (epitopepredict.base.BasicMHCIPredictor method)
(epitopepredict.base.IEDBMHCIIPredictor method)
(epitopepredict.base.IEDBMHCIPredictor method)
(epitopepredict.base.NetMHCIIPanPredictor method)
(epitopepredict.base.NetMHCPanPredictor method)
(epitopepredict.base.Predictor method)
print_heading() (epitopepredict.base.Predictor method)
print_help() (in module epitopepredict.neo)
print_options() (in module epitopepredict.config)
promiscuous_binders() (epitopepredict.base.Predictor method)
protein_summary() (epitopepredict.base.Predictor method)
(in module epitopepredict.base)
proteins() (epitopepredict.base.Predictor method)
Q
quit() (epitopepredict.tests.PredictorTests method)
R
randomize_dataframe() (in module epitopepredict.analysis)
ranked_binders() (epitopepredict.base.Predictor method)
read_defaults() (in module epitopepredict.base)
read_iedb() (in module epitopepredict.utilities)
read_names() (in module epitopepredict.neo)
read_result() (epitopepredict.base.NetMHCIIPanPredictor method)
(epitopepredict.base.NetMHCPanPredictor method)
read_result_legacy() (epitopepredict.base.NetMHCPanPredictor method)
reduce_alleles() (in module epitopepredict.tepitope)
remote_blast() (in module epitopepredict.sequtils)
reorder_filenames() (in module epitopepredict.utilities)
reshape() (epitopepredict.base.Predictor method)
reshape_data() (in module epitopepredict.base)
results_from_csv() (in module epitopepredict.base)
rmse() (in module epitopepredict.utilities)
run() (epitopepredict.neo.NeoEpitopeWorkFlow method)
(in module epitopepredict.tests)
run_vep() (in module epitopepredict.neo)
S
save() (epitopepredict.base.Predictor method)
save_msgpack() (epitopepredict.base.Predictor method)
save_to_excel() (in module epitopepredict.analysis)
score_peptide() (in module epitopepredict.tepitope)
score_peptides() (in module epitopepredict.neo)
search_pubmed() (in module epitopepredict.utilities)
self_matches() (in module epitopepredict.neo)
self_similarity() (in module epitopepredict.neo)
seq_from_binders() (in module epitopepredict.base)
seqdepot_to_coords() (in module epitopepredict.plotting)
seqs_to_dataframe() (epitopepredict.base.Predictor method)
sequence_from_peptides() (in module epitopepredict.base)
sequence_to_html_grid() (in module epitopepredict.web)
sequences_to_html_table() (in module epitopepredict.web)
set_netmhcpan_cmd() (in module epitopepredict.base)
setup() (epitopepredict.neo.NeoEpitopeWorkFlow method)
setUp() (epitopepredict.tests.PredictorTests method)
show_alignment() (in module epitopepredict.sequtils)
show_alignment_html() (in module epitopepredict.sequtils)
show_pocket_residues() (in module epitopepredict.tepitope)
show_predictors() (in module epitopepredict.neo)
signalP() (in module epitopepredict.analysis)
similarity_score() (in module epitopepredict.tepitope)
split_peptides() (in module epitopepredict.base)
summarize() (epitopepredict.base.Predictor method)
(in module epitopepredict.base)
summarize_by_protein() (in module epitopepredict.base)
summary_plots() (in module epitopepredict.neo)
supported_lengths() (epitopepredict.base.BasicMHCIPredictor method)
(epitopepredict.base.Predictor method)
(epitopepredict.base.TEpitopePredictor method)
symmetrize() (in module epitopepredict.utilities)
T
tabbed_html() (in module epitopepredict.web)
TEpitopePredictor (class in epitopepredict.base)
test() (in module epitopepredict.analysis)
(in module epitopepredict.tepitope)
(in module epitopepredict.utilities)
(in module epitopepredict.web)
test_basicmhc1() (epitopepredict.tests.PredictorTests method)
test_classes() (epitopepredict.tests.PredictorTests method)
test_conservation() (in module epitopepredict.analysis)
test_cutoffs() (epitopepredict.tests.PredictorTests method)
test_fasta() (epitopepredict.tests.PredictorTests method)
test_features() (epitopepredict.tests.PredictorTests method)
(in module epitopepredict.analysis)
test_iedbmhc1() (epitopepredict.tests.PredictorTests method)
test_load() (epitopepredict.tests.PredictorTests method)
test_mhcflurry() (epitopepredict.tests.PredictorTests method)
test_multiproc() (epitopepredict.tests.PredictorTests method)
test_netmhcpan() (epitopepredict.tests.PredictorTests method)
test_peptide_prediction() (epitopepredict.tests.PredictorTests method)
test_peptide_utils() (epitopepredict.tests.PredictorTests method)
test_run() (in module epitopepredict.neo)
test_tepitope() (epitopepredict.tests.PredictorTests method)
testrun() (in module epitopepredict.analysis)
tmhmm() (in module epitopepredict.analysis)
V
varcode_test() (in module epitopepredict.neo)
variants_from_csv() (in module epitopepredict.neo)
venndiagram() (in module epitopepredict.utilities)
virus_matches() (in module epitopepredict.neo)
virus_similarity() (in module epitopepredict.neo)
W
write_config() (in module epitopepredict.config)
write_default_config() (in module epitopepredict.config)
write_fasta() (in module epitopepredict.base)
wt_similarity() (in module epitopepredict.neo)
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