API for hase62/Neoantimon
Neoantimon: A multifunctional R package for identification of tumor-specific neoantigens
| Global functions | |
|---|---|
| CCFP.Calc | Source code |
| CalculatePriorityScores | Man page Source code |
| CheckRequiredColumns | Source code |
| CheckRequiredFiles | Source code |
| CheckRequiredFiles2 | Source code |
| ExeNetMHCpanClass1 | Source code |
| ExeNetMHCpanClass2 | Source code |
| ExemhcflurryClass1 | Source code |
| Export_Summary_Entire_Fragments | Man page Source code |
| Export_Summary_Fragments | Man page Source code |
| Export_Summary_IndelSV | Man page Source code |
| Export_Summary_IndelSV_perFragments | Man page Source code |
| Export_Summary_SNV | Man page Source code |
| GenerateIndelSeq | Source code |
| GenerateListForCCFP | Source code |
| GenerateListForGetRNASeq | Source code |
| GenerateMutatedFragments | Source code |
| GenerateMutatedSeq | Source code |
| GenerateSVFusionSeq | Source code |
| GetRNAseq | Source code |
| GetRNAseq_indel | Source code |
| GetRatio | Source code |
| InsertMhcflurryResults | Source code |
| MainEntireRegionClass1 | Man page Source code |
| MainEntireRegionClass2 | Man page Source code |
| MainINDELClass1 | Man page Source code |
| MainINDELClass2 | Man page Source code |
| MainSNVClass1 | Man page Source code |
| MainSNVClass2 | Man page Source code |
| MainSVFUSIONClass1 | Man page Source code |
| MainSVFUSIONClass2 | Man page Source code |
| MainSeqFragmentClass1 | Man page Source code |
| MainSeqFragmentClass2 | Man page Source code |
| MergeFragmentsClass1 | Source code |
| MergeFragmentsClass2 | Source code |
| MergeINDELSVClass1 | Source code |
| MergeINDELSVClass2 | Source code |
| MergeSNVClass1 | Source code |
| MergeSNVClass2 | Source code |
| RNAExpression | Source code |
| Read_files | Source code |
| SettingNetMHCIIpan | Source code |
| SettingNetMHCpan | Source code |
| TestAnalysis | Man page Source code |
| annotation_by_vep | Source code |
| apply2 | Source code |
| apply3 | Source code |
| apply4 | Source code |
| apply_multiple_snps | Source code |
| apply_multiple_snvs | Source code |
| apply_multiple_snvs_to_indel | Source code |
| calc_ccfp | Source code |
| check_dna_validity | Source code |
| check_multiple_snps | Source code |
| check_multiple_snvs | Source code |
| check_multiple_snvs_to_indel | Source code |
| check_start_codon | Source code |
| check_stop_codon | Source code |
| check_valid_indel | Source code |
| convert_to_annovar_format_from_vep | Source code |
| cut_peptide | Source code |
| generate_fraction | Source code |
| getHLAtypes | Source code |
| get_relative_mutation_position | Source code |
| get_relative_translation_end_position | Source code |
| get_relative_translation_start_position | Source code |
| integrate_same_peptide | Source code |
| make_indel_dna | Source code |
| make_mutated_dna | Source code |
| make_mutated_peptide | Source code |
| make_normal_peptide | Source code |
| read_1col_by_fread_or_scan | Source code |
| read_data | Source code |
| read_refFlat | Source code |
| read_refmrn | Source code |
| sample_copynum | Man page |
| sample_hla_table_c1 | Man page |
| sample_hla_table_c2 | Man page |
| sample_refFlat.grch37 | Man page |
| sample_refMrna.grch37.fa | Man page |
| sample_result_INDEL_CLASS1_ALL | Man page |
| sample_result_INDEL_CLASS2_ALL | Man page |
| sample_result_SNV_CLASS1_ALL | Man page |
| sample_result_SNV_CLASS2_ALL | Man page |
| sample_result_SVFusion_CLASS1_ALL | Man page |
| sample_result_SVFusion_CLASS2_ALL | Man page |
| sample_result_SeqFragment_CLASS1_ALL | Man page |
| sample_result_SeqFragment_CLASS2_ALL | Man page |
| sample_rna_exp | Man page |
| sample_sv_bnd | Man page |
| sample_vcf.annovar | Man page |
| sample_vcf.snps | Man page |
| sample_vcf.vep | Man page |
| tryCatch2 | Source code |
