Files in hase62/Neoantimon
Neoantimon: A multifunctional R package for identification of tumor-specific neoantigens
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
Meta/.!15612!vignette.rds
Meta/vignette.rds
NAMESPACE
Neoantimon.Rproj
R/.Rhistory
R/CodonTable.R
R/ExeMHCflurry.R
R/ExeNetMHCpan.R
R/FunctionVEP.R
R/FunctionsCCFP.R
R/FunctionsCalculatePriorityScores.R
R/FunctionsCommons.R
R/FunctionsRNAExpression.R
R/GenerateIndelSeq.r
R/GenerateMutatedFragments.r
R/GenerateMutatedSeq.r
R/GenerateSVFusionSeq.R
R/InsertMhcflurryResults.R
R/MainEntireRegionClass1.R
R/MainEntireRegionClass2.R
R/MainINDELClass1.R
R/MainINDELClass2.R
R/MainSNVClass1.R
R/MainSNVClass2.R
R/MainSVFUSIONClass1.R
R/MainSVFUSIONClass2.R
R/MainSeqFragmentClass1.R
R/MainSeqFragmentClass2.R
R/MergeFragmentsClass1.R
R/MergeFragmentsClass2.R
R/MergeINDELSVClass1.R
R/MergeINDELSVClass2.R
R/MergeSNVClass1.R
R/MergeSNVClass2.R
R/Neoantimon.R
R/SummaryEntireFragments.R
R/SummaryFragments.R
R/SummaryIndelSV.R
R/SummaryIndelSV_perFragments.R
R/SummarySNV.R
R/TestAnalysis.R
README.md
data/sample_copynum.txt
data/sample_hla_table_c1.txt
data/sample_hla_table_c2.txt
data/sample_refFlat.grch37.txt
data/sample_refMrna.grch37.fa.txt
data/sample_result_INDEL_CLASS1_ALL.txt
data/sample_result_INDEL_CLASS2_ALL.txt
data/sample_result_SNV_CLASS1_ALL.txt
data/sample_result_SNV_CLASS2_ALL.txt
data/sample_result_SVFusion_CLASS1_ALL.txt
data/sample_result_SVFusion_CLASS2_ALL.txt
data/sample_result_SeqFragment_CLASS1_ALL.txt
data/sample_result_SeqFragment_CLASS2_ALL.txt
data/sample_rna_exp.txt
data/sample_sv_bnd.txt
data/sample_vcf.annovar.txt
data/sample_vcf.snps.txt
data/sample_vcf.vep.txt
doc/SampleCodeForNeoantimon.R
doc/SampleCodeForNeoantimon.html
doc/SampleCodeForNeoantimon.rmd
exe_gitupdate.sh
lib/archive/setNetMHCIIpan3.2.sh
lib/archive/setNetMHCpan3.0.sh
lib/archive/setNetMHCpan4.0.sh
lib/data.zip
lib/gencode.gene.info.v36.tsv.zip
lib/gencode.gene.v36.convert.R
lib/setNetMHCIIpan4.2.sh
lib/setNetMHCpan4.1.sh
man/.Rapp.history
man/CalculatePriorityScores.Rd
man/Export_Summary_Entire_Fragments.Rd
man/Export_Summary_Fragments.Rd
man/Export_Summary_IndelSV.Rd
man/Export_Summary_IndelSV_perFragments.Rd
man/Export_Summary_SNV.Rd
man/MainEntireRegionClass1.Rd
man/MainEntireRegionClass2.Rd
man/MainINDELClass1.Rd
man/MainINDELClass2.Rd
man/MainSNVClass1.Rd
man/MainSNVClass2.Rd
man/MainSVFUSIONClass1.Rd
man/MainSVFUSIONClass2.Rd
man/MainSeqFragmentClass1.Rd
man/MainSeqFragmentClass2.Rd
man/TestAnalysis.Rd
man/sample_copynum.Rd
man/sample_hla_table_c1.Rd
man/sample_hla_table_c2.Rd
man/sample_refFlat.grch37.Rd
man/sample_refMrna.grch37.fa.Rd
man/sample_result_INDEL_CLASS1_ALL.Rd
man/sample_result_INDEL_CLASS2_ALL.Rd
man/sample_result_SNV_CLASS1_ALL.Rd
man/sample_result_SNV_CLASS2_ALL.Rd
man/sample_result_SVFusion_CLASS1_ALL.Rd
man/sample_result_SVFusion_CLASS2_ALL.Rd
man/sample_result_SeqFragment_CLASS1_ALL.Rd
man/sample_result_SeqFragment_CLASS2_ALL.Rd
man/sample_rna_exp.Rd
man/sample_sv_bnd.Rd
man/sample_vcf.annovar.Rd
man/sample_vcf.snps.Rd
man/sample_vcf.vep.Rd
manual/Neoantimon_2.1.1.pdf
vignettes/.Rhistory
vignettes/SampleCodeForNeoantimon.R
vignettes/SampleCodeForNeoantimon.html
vignettes/SampleCodeForNeoantimon.md
vignettes/SampleCodeForNeoantimon.rmd
