griffithlab/pVACtools issues and pull requests

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

Issue - State: open - Opened by lukaas33 17 days ago - 1 comment
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 17 days ago

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

Pull Request - State: open - Opened by susannasiebert 20 days ago

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

Pull Request - State: open - Opened by susannasiebert 21 days ago - 1 comment

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

Issue - State: open - Opened by luyh-xp 21 days ago - 3 comments

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

Pull Request - State: closed - Opened by susannasiebert 22 days ago

#1144 - Update pVACview anchor figure

Pull Request - State: closed - Opened by susannasiebert 22 days ago

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

Pull Request - State: closed - Opened by susannasiebert 23 days ago

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

Issue - State: open - Opened by malachig 24 days ago - 2 comments

#1141 - Plans for adding NetTCR-2.0?

Issue - State: open - Opened by lukaas33 26 days 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 28 days 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 28 days ago

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

Issue - State: open - Opened by lukaas33 about 1 month ago - 3 comments
Labels: bug report / hotfix PR

#1137 - pVACview updates for paper review

Pull Request - State: closed - Opened by susannasiebert about 1 month ago

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

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

#1135 - Add test for proximal variant file generation

Pull Request - State: closed - Opened by susannasiebert about 1 month ago

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

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

#1133 - Remove some alleles from MHCnuggets

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

#1132 - Add funding page

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

#1131 - Add support for dog alleles for NetMHCpan

Issue - State: open - Opened by susannasiebert about 2 months ago - 1 comment

#1130 - Handle invalid pVACfuse characters by trimming sequence

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

#1129 - Add page for pVACtools courses

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

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

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

#1127 - CannotConvertValueError for vcf file

Issue - State: closed - Opened by lukaas33 2 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 2 months ago

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

Issue - State: closed - Opened by MaxMichaeler 3 months ago - 1 comment
Labels: bug report / hotfix PR

#1123 - KeyError: 'mhcflurry_processing_score'

Issue - State: closed - Opened by hangfafa 3 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 3 months ago

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

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

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

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

#1119 - BigMHC prediction not working

Issue - State: closed - Opened by giacuong171 3 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 3 months ago - 6 comments

#1117 - Updated mouse anchor data links

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

#1116 - fixing rounding issue in min-max slider

Pull Request - State: closed - Opened by evelyn-schmidt 4 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 4 months ago

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

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

#1113 - Issue/1109 Minor pVACview improvements

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

#1112 - Method for decomposing MT-WT aa sequences

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

#1111 - NetChop SSLError

Issue - State: closed - Opened by Tseng722 4 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 4 months ago - 1 comment

#1109 - Minor pVACview improvements

Issue - State: closed - Opened by susannasiebert 4 months ago

#1108 - Added new valid_algorithms command (#1106)

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

#1107 - Frameshift VEP plugin

Issue - State: closed - Opened by SirKuikka 4 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 4 months ago

#1105 - Add an option to the valid_alleles command(s) to filter output by species

Issue - State: closed - Opened by susannasiebert 4 months ago

#1104 - Zero or few results after filtering

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

#1103 - Support for custom epitope prediction algorithms

Issue - State: closed - Opened by boyangzhao 4 months ago - 2 comments

#1101 - help with pVACseq customization

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

#1100 - Reviewing PR #1062

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

#1099 - if protein_identifiers_from_label[protein_label] is not None: KeyError: 92

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

#1098 - Potential improvements to the pVACview NeoFox module

Issue - State: open - Opened by susannasiebert 5 months ago
Labels: pVACview

#1097 - Update pvacseq_vignette.rst

Pull Request - State: closed - Opened by chrisamiller 5 months ago - 1 comment

#1096 - Update pvacseq_upload.rst

Pull Request - State: closed - Opened by chrisamiller 5 months ago - 1 comment

#1095 - Update pvacseq_features.rst

Pull Request - State: closed - Opened by chrisamiller 5 months ago - 1 comment

#1094 - Fix incorrect transcript2 parsing from Arriba

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

#1093 - Consider integration of MixMHCPred2

Issue - State: open - Opened by malachig 6 months ago - 3 comments

#1092 - Version of tools used in pVacFuse

Issue - State: closed - Opened by min-codes 6 months ago - 2 comments

#1091 - Generate protein fasta prox vars

Pull Request - State: closed - Opened by evelyn-schmidt 6 months ago

#1090 - Prefilter pVACseq and pVACsplice on a user-defined list of biotypes

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

#1089 - Output a visual representation of the graph after all spacers have been tested

Issue - State: open - Opened by susannasiebert 6 months ago
Labels: pVACvector

#1088 - Outputting accounted-for germline variants

Issue - State: closed - Opened by evelyn-schmidt 6 months ago - 1 comment
Labels: pVACseq

#1087 - Fix various pVACvector issues

Issue - State: open - Opened by susannasiebert 6 months ago
Labels: pVACvector

#1086 - Ensure that elution and immunogenicity percentile data is included in pVACview %ile violin plot

Issue - State: open - Opened by susannasiebert 6 months ago
Labels: pVACview

#1085 - Traceback (most recent call last): change_permissions_recursive

Issue - State: closed - Opened by xmy1990 7 months ago - 9 comments

#1084 - pVACtools not working with newest tensorflow (2.16.1)

Issue - State: closed - Opened by Stikus 7 months ago - 7 comments
Labels: bug report / hotfix PR

#1083 - Update to version 4.1.1

Pull Request - State: closed - Opened by susannasiebert 7 months ago

#1082 - Fix issue where method to determine matched wt result didn't return where appropriate

Pull Request - State: closed - Opened by susannasiebert 7 months ago

#1081 - ValueError: invalid literal for int() with base 10: ''

Issue - State: closed - Opened by ahkamzifo 7 months ago - 3 comments

#1080 - OSError: [Errno 9] Bad file descriptor

Issue - State: closed - Opened by ahkamzifo 7 months ago - 7 comments

#1079 - Handle nan values in the Mutation Position column

Pull Request - State: closed - Opened by susannasiebert 7 months ago

#1078 - Write DeepImmuno outputs to unique file locations

Pull Request - State: closed - Opened by susannasiebert 7 months ago

#1077 - Return list of combinatorial class II alleles in sorted order to be deterministic

Pull Request - State: closed - Opened by susannasiebert 7 months ago - 1 comment

#1076 - Restart inputs are different from past inputs

Issue - State: closed - Opened by YingYa 7 months ago - 5 comments
Labels: bug report / hotfix PR

#1075 - ValueError: dict contains fields not in fieldnames: 'DeepImmuno WT IC50 Score', 'DeepImmuno MT IC50 Score'

Issue - State: closed - Opened by YingYa 7 months ago - 8 comments
Labels: bug report / hotfix PR

#1074 - TypeError: argument of type 'float' is not iterable

Issue - State: closed - Opened by YingYa 7 months ago - 3 comments
Labels: bug report / hotfix PR

#1073 - Update pVACview demo data download links GitHub commit

Pull Request - State: closed - Opened by susannasiebert 7 months ago

#1072 - Fix typo

Pull Request - State: closed - Opened by susannasiebert 7 months ago

#1071 - Fix blurry pVACvector visualization images

Pull Request - State: closed - Opened by susannasiebert 7 months ago

#1070 - Remove BigMHC and DeepImmuno as direct dependencies

Pull Request - State: closed - Opened by susannasiebert 7 months ago

#1069 - DISPLAY variable issue when running pvacvector visualize

Issue - State: open - Opened by Yonghao-Holden 7 months ago - 2 comments
Labels: bug report / hotfix PR

#1068 - Update demo data, example data, and documentation for upcoming 4.1.0 release

Pull Request - State: closed - Opened by susannasiebert 7 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 8 months ago - 1 comment
Labels: bug report / hotfix PR

GitHub / griffithlab/pVACtools issues and pull requests