griffithlab pVACtools issues

griffithlab / pVACtools

http://www.pvactools.org

BSD 3-Clause Clear License

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Transcript in set

#1038 evelyn-schmidt closed 8 months ago
1
Error occurs if there are no transcripts in set

#1037 evelyn-schmidt closed 7 months ago
1
Fix bug that resulted in the TSL getting incorrectly evaluated when determining the best peptide

#1036 susannasiebert closed 10 months ago
0
pVACseq submits too big of a file to NetMHCstab server?

#1035 mantczakaus closed 10 months ago
4
Where there are multiple transcript sets in pVACview, select the one containing the top peptide

#1034 malachig closed 6 months ago
2
How does pvacfues derive the START/STOP of fusion transcript that "resulted" in a peptide?

#1033 min-codes closed 7 months ago
7
What is the standard input for gene expression for pVACtools?

#1032 PierreLaplante closed 8 months ago
2
ERROR: There was a mismatch between the actual wildtype amino acid sequence (G) and the expected amino acid sequence (A).

#1031 PierreLaplante closed 8 months ago
2
Expose per-allele, per-position anchor contribution weights to pVACview

#1030 susannasiebert closed 6 months ago
0
Investigate PRIME prediction algorithm

#1029 jhundal opened 11 months ago
1
Revert "Run MHCflurry in code instead of from the command line"

#1028 susannasiebert closed 11 months ago
0
Cannot connect to the MHCstab server

#1027 Histidine127 closed 9 months ago
2
Temporary directory for pvacseq

#1026 ysbioinfo closed 9 months ago
5
ref-transcript-mismatch-reporter ZeroDivisionError: float division by zero

#1025 weilinwu97 closed 11 months ago
1
pVACseq TypeError: ‘<’ not supported between instances of ‘float’ and ‘str’

#1024 weilinwu97 closed 9 months ago
8
cannot get same peptide in result

#1023 Tseng722 closed 9 months ago
2
Handle transcript extraction from index more generically and handle non-human alleles in pVACview

#1022 susannasiebert closed 12 months ago
0
Investigate DeepImmuno

#1021 malachig closed 6 months ago
0
Docker image to run pvacview on GCP

#1020 Layth17 closed 6 months ago
1
IEDB_MHC_II-3.1.9 installation error

#1019 serge2016 closed 9 months ago
5
pvactools reports different EL rank from NetMHCpan 4.1

#1018 ysbioinfo closed 12 months ago
4
Update reference proteome similarity step to work with nonhuman data

#1017 susannasiebert closed 1 year ago
0
Investigate DeepHLApan prediction algorithm

#1016 susannasiebert opened 1 year ago
0
During reference proteome similarity step, handle cases where a variant's full peptide sequence is not in the fasta file

#1015 susannasiebert closed 1 year ago
0
pVacFuse output filtered.tsv column description

#1014 min-codes closed 7 months ago
5
Ensure that pVACview evaluations are reset when new files are loaded

#1013 susannasiebert closed 6 months ago
1
Various pVACview improvements

#1012 susannasiebert closed 6 months ago
0
Better handling when none of the fusions are processable by pVACfuse

#1011 susannasiebert closed 1 year ago
0
Better handling when none of the fusions are processable by pVACfuse

#1010 susannasiebert closed 1 year ago
0
Don't use nargs in aggregate_report_evaluation parameter

#1009 susannasiebert closed 1 year ago
0
pvacseq example code from "Getting Started" page

#1008 nitishnih closed 1 year ago
4
Evaluate MHCRank for integration

#1007 malachig opened 1 year ago
0
Error in Calculating Reference Proteome Similarity: Exception: Unable to find full_peptide for variant

#1006 WLYYYYY closed 1 year ago
4
Move the information on the right side of the "Additional Peptide Information" panel into the appropriate tabs

#1005 susannasiebert closed 6 months ago
1
FileNotFoundError: [Errno 2] No such file or directory: '/home/MHC_Class_I/8/pvf_sample_98_arr.all_epitopes.tsv

#1004 min-codes closed 1 year ago
5
Handle invalid characters in Arriba input files

#1003 susannasiebert closed 1 year ago
0
update the fasta file output so the order is the same as the tsv input

#1002 mhoang22 closed 2 weeks ago
0
arriba output containing ? in peptide sequence will trigger error in manufacturability calculations

#1001 boyangzhao closed 1 year ago
1
Correctly set NA columns in pVACview export dataframe

#1000 susannasiebert closed 1 year ago
0
Implement download_wdls command

#999 susannasiebert closed 6 months ago
0
Handle edge case correctly where previous result's mutation position is a range

#998 susannasiebert closed 1 year ago
0
Handle Arriba files with empty peptide_sequence

#997 susannasiebert closed 1 year ago
0
pvacfuse error with null values for peptide_sequence

#996 boyangzhao closed 1 year ago
4
Update help text to fix some outdated wording

#995 susannasiebert closed 1 year ago
0
TypeError: argument of type 'NoneType' is not iterable

#994 dlgoode closed 1 year ago
17
Add matched WT to pVACfuse predictions

#993 susannasiebert opened 1 year ago
0
Investigate BigMHC prediction algorithm

#992 susannasiebert closed 6 months ago
0
Annotation of Gene Expression for pVACseq

#991 axelgschwind closed 1 year ago
2
FileNotFoundError: [Errno 2] No such file or directory: '/mnt/nfs01/home/p_laplante@intra.igr.fr/mhc_i/src/../method/netmhcpan-4.1-executable/netmhcpan_4_1_executable/netMHCpan'

#990 PierreLaplante closed 11 months ago
24
Update pVACview demo data

#989 susannasiebert closed 1 year ago
0

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