ambj MuPeXI issues - Githubissues

ambj / MuPeXI

MuPeXI: the mutant peptide extractor and informer, a tool for predicting neo-epitopes from tumor sequencing data.

Other

46 stars 28 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

UnboundLocalError: local variable 'geneID' referenced before assignment

#44 zyxNo1 closed 7 months ago
1
AssertionError: Allele "HLA-B*07:02" not stated in NetMHCpan output

#43 mimifp opened 11 months ago
1
Unable to access the file http://www.cbs.dtu.dk/services/MuPeXI/SupplTable1.csv described at "MuPeXI: prediction of neo-epitopes from tumor sequencing data"

#42 zhaoxiaofei opened 1 year ago
1
AssertionError: Allele "HLA-A02:01" not stated in NetMHCpan output

#41 Pchaskar opened 2 years ago
1
Reference Files for the given example VCF

#40 ALogandha opened 3 years ago
1
Mouse reference sequences

#39 samkleeman1 opened 3 years ago
0
Issue Installing MuPeXI

#38 leldershaw opened 3 years ago
2
Will MuPeXI become compatible with NetMHCpan 4.1?

#37 scyrusm opened 4 years ago
5
config.ini file for mouse

#36 immuneAI closed 4 years ago
0
Fix bug in parsing VEP output when aa change goes from 'X' to 'X'

#35 jherrero opened 5 years ago
0
where can I get the file 'reference_peptide_9.txt'?

#34 694376965 opened 5 years ago
1
gatk4.0.11.0 normal in the first and tumor in the latter, so allele frequence gives the normal sample now, a wrong value, vcf is different from the example.vcf given by the author

#33 kobejamescurry opened 5 years ago
1
is the author ambj still working on DTU?

#32 kobejamescurry closed 5 years ago
1
ps

#31 kobejamescurry closed 5 years ago
0
a big bug? the tmpClyJgf exists, but it is empty, so can not read. how should I reviese it?

#30 kobejamescurry opened 5 years ago
18
let us talk about the Monotonicity of the function calculating priority_score

#29 kobejamescurry opened 5 years ago
3
Allele_Frequency column is emitted empty

#28 ShahiRB opened 5 years ago
6
AssertionError: amino acid sequence length (80) less than mutation position 81

#27 d-henness opened 5 years ago
10
1

#26 kobejamescurry closed 5 years ago
0
NetMHCpan-4.0 need a criteria about EL, not mentioned in MuPexi，how to select?

#25 kobejamescurry closed 5 years ago
1
surprising Permission denied

#24 kobejamescurry closed 5 years ago
5
Ensembl references and VEP

#23 ambj opened 5 years ago
1
Incorrect translation of a complex mutation

#22 gilhornung opened 5 years ago
1
expand environment variables in paths

#21 smoors closed 5 years ago
3
ERROR：vep output file empty

#20 ghost opened 6 years ago
1
ERROR VEP output file empty

#19 LeeNicha closed 6 years ago
2
MuPeXI finds peptide in a transcript which is labeled as "Nonsense mediated decay"

#18 gilhornung opened 6 years ago
0
Gene symbols being split at hyphens '-'

#17 ibwoo opened 6 years ago
0
Skipping VCF compatibility subroutine

#16 acesnik closed 5 years ago
5
What does an error message mean?

#15 hsun9 closed 6 years ago
8
Variant Effect Predictor version compatibility

#14 trishorts closed 5 years ago
7
broken link for test.vcf and expression_test.vcf

#13 trishorts closed 6 years ago
5
AF ignored - GATK4 MuTect2 case-change

#12 ibwoo closed 6 years ago
1
Transition to NetMHCpan 4.0 is not documented

#11 gilhornung closed 6 years ago
2
Incorrect translation of an insertion mutation

#10 gilhornung closed 6 years ago
5
long FASTA output

#9 Phorutai closed 6 years ago
2
error about vep output file empty

#8 huangxiaogua closed 6 years ago
1
IndexError: list index out of range

#7 Phorutai closed 6 years ago
4
Assert mutated_peptide in peptide_info failed

#6 choosehappy closed 6 years ago
13
Issues when running on the web server

#5 kevin199011 closed 6 years ago
6
Transcripts do not correspond to the correct amino acid change

#4 gilhornung closed 6 years ago
3
VCF reading improvements

#3 JohnMCMa closed 6 years ago
1
Permitting console users to specify fork and assembly; minor bug fixes at the VEP stage

#2 JohnMCMa closed 7 years ago
0
Replace call to pandas's deprecated method

#1 koalive closed 7 years ago
0