griffithlab/pVACtools issues and pull requests

#1159 - Adding Gene and Transcript Expression to VCF for pVACseq

Issue - State: open - Opened by biounix 10 days ago - 6 comments

#1158 - Error: No command specified

Issue - State: open - Opened by Geneece 11 days ago - 1 comment

#1157 - Error

Issue - State: closed - Opened by Geneece 11 days ago
Labels: bug report / hotfix PR

#1155 - Add additional trailing amino acids for frameshift insertions when creating fasta

Pull Request - State: open - Opened by susannasiebert about 2 months ago

#1154 - [Bug report title]NoneType Error Encountered with NetMHCpan and Exception When Calling MHCflurry

Issue - State: closed - Opened by anomibo 2 months ago - 3 comments
Labels: bug report / hotfix PR

#1153 - Fix bug where the incorrect neoantigen fasta entry was used for ref proteome search

Pull Request - State: open - Opened by susannasiebert 2 months ago

#1152 - Help with MT-WT epitope match for inframe mutations

Issue - State: open - Opened by KhacDuyNguyen0 2 months ago - 4 comments

#1151 - BigMHC and DeepImmuno future support

Issue - State: closed - Opened by Stikus 2 months ago - 5 comments

#1150 - `ValueError: substring not found` when running proteome similarity search with pvacseq

Issue - State: open - Opened by lukaas33 2 months ago - 2 comments
Labels: bug report / hotfix PR

#1149 - Update pVACview percentile plots to include percentiles from elution and immunogenicity algorithms

Pull Request - State: open - Opened by susannasiebert 2 months ago

#1148 - Add new alleles that weren't previously supported

Pull Request - State: open - Opened by susannasiebert 3 months ago

#1147 - Fix aggregate inclusion binding threshold and add new --aggregate-inclusion-count-limit parameter

Pull Request - State: open - Opened by susannasiebert 3 months ago - 1 comment

#1146 - MHC allele supported by the original prediction method, but not recognized by pvacseq

Issue - State: open - Opened by luyh-xp 3 months ago - 3 comments

#1145 - Update class II pVACview demo data to match updated allele handling

Pull Request - State: closed - Opened by susannasiebert 3 months ago

#1144 - Update pVACview anchor figure

Pull Request - State: closed - Opened by susannasiebert 3 months ago

#1143 - Don't write extra title line to excel export spreadsheets

Pull Request - State: closed - Opened by susannasiebert 3 months ago

#1142 - Allow passing candidates to be based on binding OR percentile cutoff.

Issue - State: open - Opened by malachig 3 months ago - 2 comments

#1141 - Plans for adding NetTCR-2.0?

Issue - State: open - Opened by lukaas33 3 months ago - 1 comment

#1140 - Update pVACview documentation (vignette) and pVACview Tutorials page to mention anchor weights and anchor distribution tables

Issue - State: open - Opened by susannasiebert 3 months ago
Labels: documentation

#1139 - Fix issue where class ii alleles were filtered out as invalid before combining alpha and beta chains

Pull Request - State: closed - Opened by susannasiebert 3 months ago

#1138 - The .aggregated.metrics.json file is not always generated

Issue - State: open - Opened by lukaas33 3 months ago - 3 comments
Labels: bug report / hotfix PR

#1137 - pVACview updates for paper review

Pull Request - State: closed - Opened by susannasiebert 3 months ago

#1136 - Bump setuptools from 57.4.0 to 70.0.0 in /docs

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago - 1 comment
Labels: dependencies

#1135 - Add test for proximal variant file generation

Pull Request - State: closed - Opened by susannasiebert 3 months ago

#1134 - Allow aggregated TSV as an input to pvacfuse generate_protein_fasta command

Pull Request - State: closed - Opened by susannasiebert 3 months ago

#1133 - Remove some alleles from MHCnuggets

Pull Request - State: closed - Opened by susannasiebert 4 months ago

#1132 - Add funding page

Pull Request - State: closed - Opened by susannasiebert 4 months ago

#1131 - Add support for dog alleles for NetMHCpan

Issue - State: open - Opened by susannasiebert 4 months ago - 1 comment

#1130 - Handle invalid pVACfuse characters by trimming sequence

Pull Request - State: closed - Opened by susannasiebert 4 months ago

#1129 - Add page for pVACtools courses

Pull Request - State: closed - Opened by susannasiebert 4 months ago

#1128 - pVACview: neofox_ui.R and custom_ui.R not found in the output folder

Issue - State: closed - Opened by LukaszGraff 4 months ago - 2 comments
Labels: bug report / hotfix PR

#1127 - CannotConvertValueError for vcf file

Issue - State: closed - Opened by lukaas33 4 months ago - 2 comments
Labels: bug report / hotfix PR

#1126 - Add new pVACview R files to the list of files getting copied into the pVACseq output folder

Pull Request - State: closed - Opened by susannasiebert 4 months ago

#1125 - pVACFuse: KeyError: '25.GCN1-MSI1.ENST00000300648.7-ENST00000257552.7.inframe_fusion.32'

Issue - State: closed - Opened by MaxMichaeler 5 months ago - 1 comment
Labels: bug report / hotfix PR

#1123 - KeyError: 'mhcflurry_processing_score'

Issue - State: closed - Opened by hangfafa 5 months ago - 5 comments
Labels: bug report / hotfix PR

#1122 - Remove unused code in the Frameshift.pm VEP plugin

Pull Request - State: closed - Opened by susannasiebert 5 months ago

#1121 - Skip variants where VEP didn't predict an amino acid change

Pull Request - State: closed - Opened by susannasiebert 5 months ago

#1120 - CannotConvertValue: 125,142 cannot be converted to Integer, keeping as string

Issue - State: closed - Opened by dincerkilic 5 months ago - 2 comments
Labels: bug report / hotfix PR

#1119 - BigMHC prediction not working

Issue - State: closed - Opened by giacuong171 5 months ago - 3 comments
Labels: bug report / hotfix PR

#1118 - pVACseq: Discrepancy between {sample_id}.all_epitopes.tsv and {sample_id}.fasta ?

Issue - State: open - Opened by yiolino 5 months ago - 6 comments

#1117 - Updated mouse anchor data links

Pull Request - State: closed - Opened by ldhtnp 5 months ago

#1116 - fixing rounding issue in min-max slider

Pull Request - State: closed - Opened by evelyn-schmidt 5 months ago - 2 comments

#1115 - Only check for refseq_select_prot blast db species compatibility if ref proteome similarity step is run with blast

Pull Request - State: closed - Opened by susannasiebert 6 months ago

#1114 - Output anchor positions currently applied to the data in pVACview

Pull Request - State: closed - Opened by susannasiebert 6 months ago

#1113 - Issue/1109 Minor pVACview improvements

Pull Request - State: closed - Opened by ldhtnp 6 months ago

#1112 - Method for decomposing MT-WT aa sequences

Issue - State: closed - Opened by nttvy 6 months ago - 4 comments

#1111 - NetChop SSLError

Issue - State: closed - Opened by Tseng722 6 months ago - 1 comment
Labels: bug report / hotfix PR

#1110 - Added support for mouse specific allele anchor positions

Pull Request - State: closed - Opened by ldhtnp 6 months ago - 1 comment

#1109 - Minor pVACview improvements

Issue - State: closed - Opened by susannasiebert 6 months ago

#1108 - Added new valid_algorithms command (#1106)

Pull Request - State: closed - Opened by ldhtnp 6 months ago

#1107 - Frameshift VEP plugin

Issue - State: closed - Opened by SirKuikka 6 months ago - 6 comments
Labels: bug report / hotfix PR

#1106 - Implement new command `pvacseq valid_algorithms` to see which prediction algorithms support a specific allele and/or species

Issue - State: closed - Opened by susannasiebert 6 months ago

#1067 - FutureWarning: Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first

Issue - State: closed - Opened by Stikus 9 months ago - 1 comment
Labels: bug report / hotfix PR

GitHub / griffithlab/pVACtools issues and pull requests