Files in tangshao2016/neoantigenR
neoantigen prediction from NGS sequencing data
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/.Rhistory
R/alignment.R
R/antigenUtil.R
R/conf.R
R/neoantigenR.R
R/neoantigenR.orig.11082017.R
inst/extdata/Homo_sapiens.GRCh38.90.ensembl.gff3
inst/extdata/IFITM2.NA.F614.Ref1.pacbio.dnaseq.protein.msa.txt
inst/extdata/IFITM2.NA.F656.Ref1.pacbio.dnaseq.protein.msa.txt
inst/extdata/IFITM2.pacbio.dnaseq.protein.sequence.txt
inst/extdata/IFITM2_PacBio.isoforms.pdf
inst/extdata/JUND.PB.4705.3.F17.Ref1.pacbio.dnaseq.protein.msa.txt
inst/extdata/JUND.pacbio.dnaseq.protein.sequence.txt
inst/extdata/JUND_PacBio.isoforms.pdf
inst/extdata/PITPNM1.isoform.png
inst/extdata/PITPNM1.msa.pdf
inst/extdata/PITPNM1.pacbio.dnaseq.protein.msa.txt
inst/extdata/PITPNM1.pacbio.dnaseq.protein.sequence.txt
inst/extdata/PITPNM1_Exons.png
inst/extdata/PITPNM1_Exons_Cartoon.png
inst/extdata/bedtool.intersect.overlaps.txt
inst/extdata/example.RData
inst/extdata/flowchart.png
inst/extdata/gencode.v19.annotation.gff3
inst/extdata/model.gff
inst/extdata/msa.jpg
inst/extdata/msa.png
inst/extdata/putative_neoantigen_candidate_sequences.fasta
inst/extdata/putative_neoantigen_candidates.txt
inst/extdata/swissuniprots.fasta
inst/extdata/uniprot-taxonomy%3A9606.fasta
man/att.info.Rd
man/chosen.column.indicies.Rd
man/compute.database.exon.details.Rd
man/compute.query.exon.details.Rd
man/coverage.file.Rd
man/dataDir.Rd
man/find.indels.location.by.location.Rd
man/gene.df.pacbio.Rd
man/gff.file.Rd
man/gff.names.Rd
man/mainDir.Rd
man/max.mismatch.size.Rd
man/min.mismatch.size.Rd
man/minimum.flanking.region.size.Rd
man/minimum.sequence.similarity.Rd
man/neoantigenR.get.Model.Rd
man/neoantigenR.get.peptides.Rd
man/neoantigenR.initialize.Rd
man/neoantigenR.write.Rd
man/org.Rd
man/output.folder.Rd
man/pacbio.gencode.overlapping.file.Rd
man/pacbio.gff.Rd
man/pacbio.isof.ids.Rd
man/percOverlap.Rd
man/protein.database.file.name.Rd
man/reference.gff.Rd
man/reference.gff.file.Rd
man/reference.gff.info.Rd
man/reference.gff.info.chosen.Rd
man/refseq.pacbio.name.ids.Rd
man/retrieve.geneName.pacbioID.mapping.v2.Rd
man/sample.pacbio.gencode.id.mapping.Rd
man/target.gene.list.Rd
man/uniprot.human.database.Rd
man/uniprot.protein.names.new.Rd
man/uniprot.protein.swissprot.index.Rd
man/use.reference.annotation.gff.Rd
man/validate.in.database.boolean.Rd
man/write.dna.seq.by.reference.genome.Rd
man/write.dna.sequence.reference.Rd
myFirstAlignment.tex
neoantigenR.Rproj
vignettes/neoantigenR.Rmd
vignettes/neoantigenR.html
