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Hunting for T-cell epitopes in recurrent NUTM1 somatic fusions

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pirl-unc/nutm1-fusions

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18 Commits
aso-design
aso-design
 
 
diagram
diagram
 
 
french-expression
french-expression
 
 
hpa
hpa
 
 
hunt-for-more-targets
hunt-for-more-targets
 
 
mhcflurry
mhcflurry
 
 
nutm1-ctag
nutm1-ctag
 
 
.gitignore
.gitignore
 
 
15mer-peptides-vs-number-alleles.png
15mer-peptides-vs-number-alleles.png
 
 
15mer-peptides-vs-population-coverage.png
15mer-peptides-vs-population-coverage.png
 
 
2023-10-30_UNC_IMPX_Biognosys_Results.xlsx
2023-10-30_UNC_IMPX_Biognosys_Results.xlsx
 
 
Analyze MHC predictions for NUTM1 from exon 2.ipynb
Analyze MHC predictions for NUTM1 from exon 2.ipynb
 
 
Catalog of fusion partners.ipynb
Catalog of fusion partners.ipynb
 
 
Create fusion junction FASTA.ipynb
Create fusion junction FASTA.ipynb
 
 
Does MHCflurry predict the mass spec hits?.ipynb
Does MHCflurry predict the mass spec hits?.ipynb
 
 
Generate all peptides for MHCflurry spanning fusion sequences.ipynb
Generate all peptides for MHCflurry spanning fusion sequences.ipynb
 
 
Generate fusion proteins.ipynb
Generate fusion proteins.ipynb
 
 
Graph eigenvalues.ipynb
Graph eigenvalues.ipynb
 
 
LICENSE
LICENSE
 
 
NUTM1 predictions.ipynb
NUTM1 predictions.ipynb
 
 
README.md
README.md
 
 
all-fusion-spanning-peptide-predictions-by-source.png
all-fusion-spanning-peptide-predictions-by-source.png
 
 
all-fusion-spanning-peptide-predictions.png
all-fusion-spanning-peptide-predictions.png
 
 
cell-line-alleles-balbc-mouse.csv
cell-line-alleles-balbc-mouse.csv
 
 
cell-line-alleles.csv
cell-line-alleles.csv
 
 
common-hla-alleles.csv
common-hla-alleles.csv
 
 
fusion-2-cell-line-alleles.csv
fusion-2-cell-line-alleles.csv
 
 
fusion-junction-peptide-predictions.csv
fusion-junction-peptide-predictions.csv
 
 
fusion-peptide-cell-line-alleles.csv
fusion-peptide-cell-line-alleles.csv
 
 
fusion-spanning-peptide.csv
fusion-spanning-peptide.csv
 
 
netmhcpan4.1-nutm1.csv
netmhcpan4.1-nutm1.csv
 
 
nutm1-fusion-sequences-compact.csv
nutm1-fusion-sequences-compact.csv
 
 
nutm1-fusion-sequences.csv
nutm1-fusion-sequences.csv
 
 
nutm1-fusion-sequences.fasta
nutm1-fusion-sequences.fasta
 
 
nutm1-peptides-in-iedb.csv
nutm1-peptides-in-iedb.csv
 
 
predictions-fusion-junction-BRD4-exon-13-NUTM1-exon-3.csv
predictions-fusion-junction-BRD4-exon-13-NUTM1-exon-3.csv
 
 
predictions-fusion-junction.csv
predictions-fusion-junction.csv
 
 
predictions.csv
predictions.csv
 
 
run-mhcflurry-fusion-junction-BRD4-exon-12-NUTM1-exon-2.sh
run-mhcflurry-fusion-junction-BRD4-exon-12-NUTM1-exon-2.sh
 
 
run-mhcflurry-fusion-junction-BRD4-exon-13-NUTM1-exon-3.sh
run-mhcflurry-fusion-junction-BRD4-exon-13-NUTM1-exon-3.sh
 
 
run-mhcflurry-fusion-junctions.sh
run-mhcflurry-fusion-junctions.sh
 
 
run-mhcflurry-nutm1-cell-lines-fusion-peptide-2.sh
run-mhcflurry-nutm1-cell-lines-fusion-peptide-2.sh
 
 
run-mhcflurry-nutm1-cell-lines-fusion-peptide.sh
run-mhcflurry-nutm1-cell-lines-fusion-peptide.sh
 
 
run-mhcflurry-nutm1-cell-lines-mouse.sh
run-mhcflurry-nutm1-cell-lines-mouse.sh
 
 
run-mhcflurry-nutm1-cell-lines.sh
run-mhcflurry-nutm1-cell-lines.sh
 
 
run-mhcflurry.sh
run-mhcflurry.sh
 
 
top-fusion-spanning-peptide-predictions-by-source.png
top-fusion-spanning-peptide-predictions-by-source.png
 
 
top-predictions-by-allele.png
top-predictions-by-allele.png
 
 
top-predictions-by-gene.png
top-predictions-by-gene.png
 
 

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nutm1-fusions

Hunting for T-cell epitopes in recurrent NUTM1 somatic fusions

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Hunting for T-cell epitopes in recurrent NUTM1 somatic fusions

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