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76 Open 554 Closed
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Issues list

If the best peptide in the aggregate report doesn't meet the aggregate inclusion threshold, still include its metadata in the metrics.json file
#1166 opened Dec 18, 2024 by susannasiebert 5.1.0
Prevent pVACvector from clipping epitopes pVACvector
#1164 opened Dec 16, 2024 by susannasiebert 5.1.0
Error: No command specified bug report / hotfix PR
#1158 opened Nov 19, 2024 by Geneece
4
Allow passing candidates to be based on binding OR percentile cutoff.
#1142 opened Sep 9, 2024 by malachig 5.1.0
2
Plans for adding NetTCR-2.0?
#1141 opened Sep 7, 2024 by lukaas33
1
Update pVACview documentation (vignette) and pVACview Tutorials page to mention anchor weights and anchor distribution tables documentation
#1140 opened Sep 5, 2024 by susannasiebert 5.1.0
1
Add a warning message when no binding algorithm was chosen to indicate that no .aggregated.metrics.json file will be generated
#1138 opened Aug 28, 2024 by lukaas33 5.1.0
1
@ldhtnp
3
pVACseq: Discrepancy between {sample_id}.all_epitopes.tsv and {sample_id}.fasta ? bug report / hotfix PR
#1118 opened Jun 26, 2024 by yiolino
8
Potential improvements to the pVACview NeoFox module pVACview
#1098 opened Apr 30, 2024 by susannasiebert
4 of 13 tasks
Consider integration of MixMHCPred2
#1093 opened Apr 15, 2024 by malachig
3
Output a visual representation of the graph after all spacers have been tested pVACvector
#1089 opened Apr 5, 2024 by susannasiebert 5.1.0
1
QUESTION: How to integrate netchop results to aditionnally filter possible peptides
#1064 opened Feb 19, 2024 by PierreLaplante
Overview of possible new prediction algorithms and their installation/run requirements
#1056 opened Jan 26, 2024 by susannasiebert
Consider integration with ACE a tool for generation of ELISpot configurations (peptide-pool assignments)
#1051 opened Jan 16, 2024 by malachig
Investigate PRIME prediction algorithm
#1029 opened Sep 25, 2023 by jhundal
1
Investigate DeepHLApan prediction algorithm grant
#1016 opened Aug 9, 2023 by susannasiebert
Evaluate MHCRank for integration
#1007 opened Jul 24, 2023 by malachig 5.1.0
Add matched WT to pVACfuse predictions grant
#993 opened Jul 6, 2023 by susannasiebert 5.1.0
Investigate Pepsickle as an alternative to NetChop
#986 opened Jun 22, 2023 by susannasiebert 5.1.0
Update reference proteome analysis to consider patient genotype grant
#948 opened Apr 7, 2023 by malachig
3
Create helper tool that generates information for a peptide order form grant
#947 opened Apr 5, 2023 by malachig 5.1.0
Should anchor position be a criteria in the aggregate reprot for class II predictions? grant
#940 opened Mar 29, 2023 by susannasiebert
1
Further improve selection of best epitope in aggregate report grant
#912 opened Mar 7, 2023 by susannasiebert 5.1.0
Implement a --ignore-rna-in-tiering flag
#910 opened Mar 6, 2023 by susannasiebert
Incorporate better handling of HLA allele-specific expression loss grant
#901 opened Feb 14, 2023 by malachig
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