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BA_another_data
BA_another_data
 
 
NetMHCIIpan_train
NetMHCIIpan_train
 
 
.DS_Store
.DS_Store
 
 
15mer_CNN_result.csv
15mer_CNN_result.csv
 
 
15mer_DNN_result.csv
15mer_DNN_result.csv
 
 
15mer_data.csv
15mer_data.csv
 
 
15mer_pep_only.txt
15mer_pep_only.txt
 
 
15mer_rank_result.csv
15mer_rank_result.csv
 
 
15mer_result.csv
15mer_result.csv
 
 
30_mut_ccf_tpm_neo.rds
30_mut_ccf_tpm_neo.rds
 
 
30_neo_es.rds
30_neo_es.rds
 
 
30_sim_add_cancer.rds
30_sim_add_cancer.rds
 
 
Automated_benchmark.csv
Automated_benchmark.csv
 
 
Automated_benchmark_filter.csv
Automated_benchmark_filter.csv
 
 
BA_Automated_prediction_result.csv
BA_Automated_prediction_result.csv
 
 
BA_MHC_label.csv
BA_MHC_label.csv
 
 
BA_allele.csv
BA_allele.csv
 
 
BLOSUM62.csv
BLOSUM62.csv
 
 
Blosum62.py
Blosum62.py
 
 
DF15.csv
DF15.csv
 
 
IEDB_CD4_tools_manually.csv
IEDB_CD4_tools_manually.csv
 
 
IEDB_MHCII_immuno.csv
IEDB_MHCII_immuno.csv
 
 
IEDB_MHCII_immuno_allele.csv
IEDB_MHCII_immuno_allele.csv
 
 
IEDB_benchmark.csv
IEDB_benchmark.csv
 
 
IEDB_benchmark_result.csv
IEDB_benchmark_result.csv
 
 
IEDB_benchmark_result_noba.csv
IEDB_benchmark_result_noba.csv
 
 
IEDB_benchmark_with_random.csv
IEDB_benchmark_with_random.csv
 
 
IEDB_benchmark_with_random_new.csv
IEDB_benchmark_with_random_new.csv
 
 
IMM_bg_pep.csv
IMM_bg_pep.csv
 
 
IMM_data_random2.csv
IMM_data_random2.csv
 
 
MHCIBA_IMM.rds
MHCIBA_IMM.rds
 
 
MHCIIBA_IMM.rds
MHCIIBA_IMM.rds
 
 
NN_data.py
NN_data.py
 
 
README
README
 
 
allele.csv
allele.csv
 
 
another_machine_learning.npy
another_machine_learning.npy
 
 
cancer_type.csv
cancer_type.csv
 
 
driver_mutations.rds
driver_mutations.rds
 
 
example.csv
example.csv
 
 
iedb_repitope.csv
iedb_repitope.csv
 
 
kmer_CNN_result.csv
kmer_CNN_result.csv
 
 
kmer_DNN_result.csv
kmer_DNN_result.csv
 
 
kmer_data.csv
kmer_data.csv
 
 
kmer_pep_only.csv
kmer_pep_only.csv
 
 
kmer_rank_result.csv
kmer_rank_result.csv
 
 
kmer_result.csv
kmer_result.csv
 
 
mhcii_initial_benchmark_datasets.tsv
mhcii_initial_benchmark_datasets.tsv
 
 
mixMHC2pred_Auto_filter_ba_result.csv
mixMHC2pred_Auto_filter_ba_result.csv
 
 
mixMHC2pred_Automated.csv
mixMHC2pred_Automated.csv
 
 
model_test.csv
model_test.csv
 
 
model_test_TLimmuno2.csv
model_test_TLimmuno2.csv
 
 
model_test_ba.csv
model_test_ba.csv
 
 
model_test_el.csv
model_test_el.csv
 
 
model_test_iedb.csv
model_test_iedb.csv
 
 
model_test_netMHCIIpan.csv
model_test_netMHCIIpan.csv
 
 
model_test_pep.csv
model_test_pep.csv
 
 
model_test_repitope.csv
model_test_repitope.csv
 
 
mut_all.rds
mut_all.rds
 
 
mut_ccf_tpm_neo.rds
mut_ccf_tpm_neo.rds
 
 
nature_HLA.csv
nature_HLA.csv
 
 
nature_immuno_rate.pdf
nature_immuno_rate.pdf
 
 
nature_peptide.csv
nature_peptide.csv
 
 
neo_es.rds
neo_es.rds
 
 
neoantigen.csv
neoantigen.csv
 
 
neoantigen_pro.csv
neoantigen_pro.csv
 
 
neoantigen_result.csv
neoantigen_result.csv
 
 
netMHCIIpan_15_mer_ba.csv
netMHCIIpan_15_mer_ba.csv
 
 
netMHCIIpan_15_mer_el.csv
netMHCIIpan_15_mer_el.csv
 
 
netMHCIIpan_Auto_filter_allele_ba_result.csv
netMHCIIpan_Auto_filter_allele_ba_result.csv
 
 
netMHCIIpan_Auto_filter_ba_result.csv
netMHCIIpan_Auto_filter_ba_result.csv
 
 
netMHCIIpan_IEDB_ba.csv
netMHCIIpan_IEDB_ba.csv
 
 
netMHCIIpan_IEDB_el.csv
netMHCIIpan_IEDB_el.csv
 
 
netMHCIIpan_k_mer_ba.csv
netMHCIIpan_k_mer_ba.csv
 
 
netMHCIIpan_k_mer_el.csv
netMHCIIpan_k_mer_el.csv
 
 
net_neo_es.rds
net_neo_es.rds
 
 
pep.csv
pep.csv
 
 
pep_only.txt
pep_only.txt
 
 
pep_result.csv
pep_result.csv
 
 
peptide.csv
peptide.csv
 
 
position.npy
position.npy
 
 
position_ala.npy
position_ala.npy
 
 
position_ala_BA.npy
position_ala_BA.npy
 
 
position_zero_BA.npy
position_zero_BA.npy
 
 
pseudosequence.2016.all.X.dat
pseudosequence.2016.all.X.dat
 
 
repitope_15mer_result.csv
repitope_15mer_result.csv
 
 
uniport_human.fasta
uniport_human.fasta
 
 

README

There are some data file are too large to put it in Github, so we will share it by Google Driver: https://drive.google.com/drive/folders/12-CR1PGdwlU_c0bdCyNVTjsXmH7K5-ix?usp=sharing.