griffithlab/pVACtools

Issues

• Prefilter pVACseq and pVACsplice on a user-defined list of biotypes

  #1090 opened 9 months ago by susannasiebert
  3

• [Bug report title]NoneType Error Encountered with NetMHCpan and Exception When Calling MHCflurry

  #1154 opened 3 months ago by anomibo
  3

• BigMHC and DeepImmuno future support

  #1151 opened 3 months ago by Stikus
  5

• Help with MT-WT epitope match for inframe mutations

  #1152 opened 4 months ago by KhacDuyNguyen0
  4

• `ValueError: substring not found` when running proteome similarity search with pvacseq

  #1150 opened 4 months ago by lukaas33
  2

• MHC allele supported by the original prediction method, but not recognized by pvacseq

  #1146 opened 4 months ago by luyh-xp
  3

• Potential improvements to the pVACview NeoFox module

  #1098 opened 9 months ago by susannasiebert
  0

• Allow passing candidates to be based on binding OR percentile cutoff.

  #1142 opened 4 months ago by malachig
  2

• Consider integration of MixMHCPred2

  #1093 opened 9 months ago by malachig
  3

• Plans for adding NetTCR-2.0?

  #1141 opened 4 months ago by lukaas33
  1

• Update pVACview documentation (vignette) and pVACview Tutorials page to mention anchor weights and anchor distribution tables

  #1140 opened 4 months ago by susannasiebert
  0

• The .aggregated.metrics.json file is not always generated

  #1138 opened 5 months ago by lukaas33
  3

• pVACseq: Discrepancy between {sample_id}.all_epitopes.tsv and {sample_id}.fasta ?

  #1118 opened 7 months ago by yiolino
  6

• Ensure that elution and immunogenicity percentile data is included in pVACview %ile violin plot

  #1086 opened 10 months ago by susannasiebert
  0

• Fix various pVACvector issues

  #1087 opened 9 months ago by susannasiebert
  0

• Frameshift VEP plugin

  #1107 opened 5 months ago by SirKuikka
  6

• pVACview: neofox_ui.R and custom_ui.R not found in the output folder

  #1128 opened 5 months ago by LukaszGraff
  2

• pVACFuse: KeyError: '25.GCN1-MSI1.ENST00000300648.7-ENST00000257552.7.inframe_fusion.32'

  #1125 opened 5 months ago by MaxMichaeler
  1

• Outputting accounted-for germline variants

  #1088 opened 5 months ago by evelyn-schmidt
  1

• Add support for dog alleles for NetMHCpan

  #1131 opened 5 months ago by susannasiebert
  1

• Support for custom epitope prediction algorithms

  #1103 opened 5 months ago by boyangzhao
  2

• Zero or few results after filtering

  #1104 opened 5 months ago by SirKuikka
  6

• CannotConvertValueError for vcf file

  #1127 opened 5 months ago by lukaas33
  2

• CannotConvertValue: 125,142 cannot be converted to Integer, keeping as string

  #1120 opened 6 months ago by dincerkilic
  2

• KeyError: 'mhcflurry_processing_score'

  #1123 opened 6 months ago by hangfafa
  5

• Method for decomposing MT-WT aa sequences

  #1112 opened 6 months ago by nttvy
  4

• BigMHC prediction not working

  #1119 opened 7 months ago by giacuong171
  3

• Implement new command `pvacseq valid_algorithms` to see which prediction algorithms support a specific allele and/or species

  #1106 opened 7 months ago by susannasiebert
  0

• NetChop SSLError

  #1111 opened 7 months ago by Tseng722
  1

• Minor pVACview improvements

  #1109 opened 7 months ago by susannasiebert
  0

• Add an option to the valid_alleles command(s) to filter output by species

  #1105 opened 7 months ago by susannasiebert
  0

• Traceback (most recent call last): change_permissions_recursive

  #1085 opened 8 months ago by xmy1990
  9

• OSError: [Errno 9] Bad file descriptor

  #1080 opened 8 months ago by ahkamzifo
  7

• Version of tools used in pVacFuse

  #1092 opened 8 months ago by min-codes
  2

• help with pVACseq customization

  #1101 opened 8 months ago by javierAPC
  2

• if protein_identifiers_from_label[protein_label] is not None: KeyError: 92

  #1099 opened 8 months ago by brycemash
  2

• Output a visual representation of the graph after all spacers have been tested

  #1089 opened 9 months ago by susannasiebert
  0

• pVACtools not working with newest tensorflow (2.16.1)

  #1084 opened 10 months ago by Stikus
  7

• Restart inputs are different from past inputs

  #1076 opened 10 months ago by YingYa
  5

• TypeError: argument of type 'float' is not iterable

  #1074 opened 10 months ago by YingYa
  3

• ValueError: dict contains fields not in fieldnames: 'DeepImmuno WT IC50 Score', 'DeepImmuno MT IC50 Score'

  #1075 opened 10 months ago by YingYa
  8

• ValueError: invalid literal for int() with base 10: ''

  #1081 opened 10 months ago by ahkamzifo
  3

• Remove "Show x entries" dropdown from "Binding Data" and "Elution Data" tabs

  #1060 opened a year ago by susannasiebert
  0

• DISPLAY variable issue when running pvacvector visualize

  #1069 opened a year ago by Yonghao-Holden
  5

• Minor fix in readme

  #1066 opened a year ago by serge2016
  3

• FutureWarning: Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first

  #1067 opened a year ago by Stikus
  1

• pVACview demo: some candidates dont show anchor heatmap

  #1059 opened a year ago by mhoang22
  1

• QUESTION: How to integrate netchop results to aditionnally filter possible peptides

  #1064 opened a year ago by PierreLaplante
  0

• ref-transcript-mismatch-reporter does not work

  #1058 opened a year ago by xmy1990
  6

• Remove "Show entries" and search box in Additional Peptide Information box / Binding Data tab

  #1061 opened a year ago by huimingx
  1