griffithlab/pVACtools issues and pull requests

#1056 - Overview of possible new prediction algorithms and their installation/run requirements

Issue - State: open - Opened by susannasiebert 10 months ago

#1055 - Add command to download WDL files

Pull Request - State: closed - Opened by susannasiebert 10 months ago

#1054 - Display pVACtools version in the footer of pVACview

Issue - State: open - Opened by susannasiebert 10 months ago
Labels: pVACview

#1053 - CalledProcessError

Issue - State: closed - Opened by ZoeChao2001 11 months ago - 3 comments
Labels: bug report / hotfix PR

#1052 - Error out when attempting to use multithreading on MacOS

Pull Request - State: closed - Opened by susannasiebert 11 months ago

#1051 - Consider integration with ACE a tool for generation of ELISpot configurations (peptide-pool assignments)

Issue - State: open - Opened by malachig 11 months ago

#1050 - Handle various IEDB outputs with incorrect data

Pull Request - State: closed - Opened by susannasiebert 11 months ago

#1049 - Retry when IEDB API returns no prediction data

Pull Request - State: closed - Opened by susannasiebert 11 months ago

#1048 - Handle output from MHCflurry when one of the percentiles is empty

Pull Request - State: closed - Opened by susannasiebert 11 months ago

#1047 - SUGGESTION Add specific anchoring residues for alleles H2-Db, Kb, Dd, Hd and Kd from https://doi.org/10.1084/jem.20190179

Issue - State: closed - Opened by PierreLaplante 11 months ago - 2 comments

#1046 - TypeError: '<' not supported between instances of 'float' and 'str'

Issue - State: closed - Opened by ZoeChao2001 11 months ago - 3 comments
Labels: bug report / hotfix PR

#1045 - Support TSL for GRCm38

Pull Request - State: closed - Opened by susannasiebert 11 months ago

#1044 - TSL level not reported (and used as a filter) in all_epitope.tsv/aggregated.tsv

Issue - State: closed - Opened by PierreLaplante 11 months ago - 5 comments
Labels: bug report / hotfix PR

#1043 - WARNING [init.py:662] did not find allele distance info from netmhcpan_output

Issue - State: closed - Opened by PierreLaplante 11 months ago - 10 comments
Labels: bug report / hotfix PR

#1042 - Fix issue with how AGFusion fusion positions are determined

Pull Request - State: closed - Opened by susannasiebert 11 months ago

#1041 - Adjust BLASTp word size to be no more than half the query sequence length

Pull Request - State: closed - Opened by susannasiebert 11 months ago

#1040 - Any plans to implement anchor binding position in pVACseq

Issue - State: closed - Opened by immuneAI 12 months ago - 2 comments

#1039 - ERROR: output_parser.py(195)match_wildtype_and_mutant_entry_for_missense() -> wt_epitope_seq = wt_result['wt_epitope_seq'] -- (Pdb)

Issue - State: closed - Opened by ZoeChao2001 about 1 year ago - 6 comments
Labels: bug report / hotfix PR

#1038 - Transcript in set

Pull Request - State: closed - Opened by evelyn-schmidt about 1 year ago - 1 comment

#1037 - Error occurs if there are no transcripts in set

Issue - State: closed - Opened by evelyn-schmidt about 1 year ago - 1 comment

#1036 - Fix bug that resulted in the TSL getting incorrectly evaluated when determining the best peptide

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

#1035 - pVACseq submits too big of a file to NetMHCstab server?

Issue - State: closed - Opened by mantczakaus about 1 year ago - 4 comments
Labels: bug report / hotfix PR

#1034 - Where there are multiple transcript sets in pVACview, select the one containing the top peptide

Issue - State: open - Opened by malachig about 1 year ago - 2 comments
Labels: pVACview

#1033 - How does pvacfues derive the START/STOP of fusion transcript that "resulted" in a peptide?

Issue - State: closed - Opened by min-codes about 1 year ago - 7 comments

#1032 - What is the standard input for gene expression for pVACtools?

Issue - State: closed - Opened by PierreLaplante about 1 year ago - 2 comments

#1031 - ERROR: There was a mismatch between the actual wildtype amino acid sequence (G) and the expected amino acid sequence (A).

Issue - State: closed - Opened by PierreLaplante about 1 year ago - 2 comments
Labels: bug report / hotfix PR

#1030 - Expose per-allele, per-position anchor contribution weights to pVACview

Issue - State: open - Opened by susannasiebert about 1 year ago
Labels: pVACview

#1029 - Investigate PRIME prediction algorithm

Issue - State: open - Opened by jhundal about 1 year ago - 1 comment

#1028 - Revert "Run MHCflurry in code instead of from the command line"

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

#1027 - Cannot connect to the MHCstab server

Issue - State: closed - Opened by Histidine127 about 1 year ago - 2 comments
Labels: bug report / hotfix PR

#1026 - Temporary directory for pvacseq

Issue - State: closed - Opened by ysbioinfo about 1 year ago - 5 comments
Labels: bug report / hotfix PR

#1025 - ref-transcript-mismatch-reporter ZeroDivisionError: float division by zero

Issue - State: closed - Opened by weilinwu97 about 1 year ago - 1 comment
Labels: bug report / hotfix PR

#1024 - pVACseq TypeError: ‘<’ not supported between instances of ‘float’ and ‘str’

Issue - State: closed - Opened by weilinwu97 about 1 year ago - 8 comments
Labels: bug report / hotfix PR

#1023 - cannot get same peptide in result

Issue - State: closed - Opened by Tseng722 about 1 year ago - 2 comments
Labels: bug report / hotfix PR

#1022 - Handle transcript extraction from index more generically and handle non-human alleles in pVACview

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

#1021 - Investigate DeepImmuno

Issue - State: open - Opened by malachig about 1 year ago

#1020 - Docker image to run pvacview on GCP

Pull Request - State: closed - Opened by Layth17 about 1 year ago - 1 comment

#1019 - IEDB_MHC_II-3.1.9 installation error

Issue - State: closed - Opened by serge2016 over 1 year ago - 5 comments
Labels: bug report / hotfix PR

#1018 - pvactools reports different EL rank from NetMHCpan 4.1

Issue - State: closed - Opened by ysbioinfo over 1 year ago - 4 comments
Labels: bug report / hotfix PR

#1017 - Update reference proteome similarity step to work with nonhuman data

Pull Request - State: closed - Opened by susannasiebert over 1 year ago

#1016 - Investigate DeepHLApan prediction algorithm

Issue - State: open - Opened by susannasiebert over 1 year ago
Labels: grant

#1015 - During reference proteome similarity step, handle cases where a variant's full peptide sequence is not in the fasta file

Pull Request - State: closed - Opened by susannasiebert over 1 year ago

#1014 - pVacFuse output filtered.tsv column description

Issue - State: closed - Opened by min-codes over 1 year ago - 5 comments

#1013 - Ensure that pVACview evaluations are reset when new files are loaded

Issue - State: closed - Opened by susannasiebert over 1 year ago - 1 comment
Labels: pVACview

#1012 - Various pVACview improvements

Pull Request - State: closed - Opened by susannasiebert over 1 year ago

#1011 - Better handling when none of the fusions are processable by pVACfuse

Pull Request - State: closed - Opened by susannasiebert over 1 year ago

#1010 - Better handling when none of the fusions are processable by pVACfuse

Pull Request - State: closed - Opened by susannasiebert over 1 year ago

#1009 - Don't use nargs in aggregate_report_evaluation parameter

Pull Request - State: closed - Opened by susannasiebert over 1 year ago

#1008 - pvacseq example code from "Getting Started" page

Issue - State: closed - Opened by nitishnih over 1 year ago - 4 comments

#1007 - Evaluate MHCRank for integration

Issue - State: open - Opened by malachig over 1 year ago

#1006 - Error in Calculating Reference Proteome Similarity: Exception: Unable to find full_peptide for variant

Issue - State: closed - Opened by WLYYYYY over 1 year ago - 4 comments
Labels: bug report / hotfix PR

#1005 - Move the information on the right side of the "Additional Peptide Information" panel into the appropriate tabs

Issue - State: open - Opened by susannasiebert over 1 year ago - 1 comment
Labels: pVACview

#1004 - FileNotFoundError: [Errno 2] No such file or directory: '/home/MHC_Class_I/8/pvf_sample_98_arr.all_epitopes.tsv

Issue - State: closed - Opened by min-codes over 1 year ago - 5 comments
Labels: bug report / hotfix PR

#1003 - Handle invalid characters in Arriba input files

Pull Request - State: closed - Opened by susannasiebert over 1 year ago

#1002 - update the fasta file output so the order is the same as the tsv input

Pull Request - State: closed - Opened by mhoang22 over 1 year ago

#1001 - arriba output containing ? in peptide sequence will trigger error in manufacturability calculations

Issue - State: closed - Opened by boyangzhao over 1 year ago - 1 comment
Labels: bug report / hotfix PR

#1000 - Correctly set NA columns in pVACview export dataframe

Pull Request - State: closed - Opened by susannasiebert over 1 year ago

#999 - Implement download_wdls command

Issue - State: open - Opened by susannasiebert over 1 year ago

#998 - Handle edge case correctly where previous result's mutation position is a range

Pull Request - State: closed - Opened by susannasiebert over 1 year ago

#997 - Handle Arriba files with empty peptide_sequence

Pull Request - State: closed - Opened by susannasiebert over 1 year ago

#996 - pvacfuse error with null values for peptide_sequence

Issue - State: closed - Opened by boyangzhao over 1 year ago - 4 comments
Labels: bug report / hotfix PR

#995 - Update help text to fix some outdated wording

Pull Request - State: closed - Opened by susannasiebert over 1 year ago

#994 - TypeError: argument of type 'NoneType' is not iterable

Issue - State: closed - Opened by dlgoode over 1 year ago - 17 comments
Labels: bug report / hotfix PR

#993 - Add matched WT to pVACfuse predictions

Issue - State: open - Opened by susannasiebert over 1 year ago
Labels: grant

#992 - Investigate BigMHC prediction algorithm

Issue - State: open - Opened by susannasiebert over 1 year ago
Labels: grant

#991 - Annotation of Gene Expression for pVACseq

Issue - State: closed - Opened by axelgschwind over 1 year ago - 2 comments
Labels: bug report / hotfix PR

#990 - FileNotFoundError: [Errno 2] No such file or directory: '/mnt/nfs01/home/[email protected]/mhc_i/src/../method/netmhcpan-4.1-executable/netmhcpan_4_1_executable/netMHCpan'

Issue - State: closed - Opened by PierreLaplante over 1 year ago - 24 comments
Labels: bug report / hotfix PR

GitHub / griffithlab/pVACtools issues and pull requests