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arkal
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Transgene
This is a repository to host the transgene tool. Transgene takes a snpeffed vcf and a peptide fasta , and returns 3 peptide fastas containing 9-, 10- and 15-mers harboring the called mutations
Apache License 2.0
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Fix same-codon bug (resolves #61)
#62
arkal
closed
6 years ago
0
New Bug in co-expressed mutants without RNA
#61
arkal
closed
6 years ago
0
Bug in co-expressed mutants without RNA
#60
arkal
closed
6 years ago
0
Completely rewrite how fusion junctions are handled
#59
arkal
closed
6 years ago
0
handle RNA-gene acceptors
#58
arkal
closed
6 years ago
1
Cherry pick from master
#57
arkal
closed
6 years ago
0
Fix logic error in read_fusions (resolves #53)
#56
arkal
closed
6 years ago
0
Fix neg strand deletion edge case (resolves #52)
#55
arkal
closed
6 years ago
0
Fix edge case in indels in repetitive regions (resolves #51)
#54
arkal
closed
6 years ago
0
transgene always rejects fusions with chrM in second partner
#53
arkal
closed
6 years ago
0
Fix edge case in deletions on the negative strand
#52
arkal
closed
6 years ago
0
Fix edge case in indels in repetitive regions
#51
arkal
closed
6 years ago
0
Fix bug with synonymous mutation in incomplete transcript (resolves #49)
#50
arkal
closed
6 years ago
0
Fix bug with Synonymous SNVS and incomplete transcripts
#49
arkal
closed
6 years ago
0
Fix bug in snvs touching same codon (resolves #47)
#48
arkal
closed
6 years ago
0
Fix error in SNVs affecting same codon
#47
arkal
closed
6 years ago
0
make a manual/readme
#46
arkal
opened
6 years ago
0
Implement support for snpeff 4.0+ and VEP (Resolves #44)
#45
arkal
closed
6 years ago
0
support for snpeff 4.0+ and vep
#44
arkal
closed
6 years ago
0
Fix bugs introduced by indel support (resolves #41, resolves #42)
#43
arkal
closed
6 years ago
0
Fix bug in indels using wrong first exon coords
#42
arkal
closed
6 years ago
0
Fix pseudo-mnp support broken by indels
#41
arkal
closed
6 years ago
0
support for MNPS
#40
arkal
opened
6 years ago
0
Make test files use git lfs
#39
arkal
opened
6 years ago
0
Add VAF info to IAR name (resolves #37)
#38
arkal
closed
6 years ago
0
add vaf information to IAR
#37
arkal
closed
6 years ago
0
Add indel support (resolves #30)
#36
arkal
closed
6 years ago
0
Filter fusion artifacts (resolves #29)
#35
arkal
closed
6 years ago
0
Handle Multi Allelic Variants (resolves #33)
#34
arkal
closed
6 years ago
0
Handle multiallelic variants
#33
arkal
closed
6 years ago
0
Fix bug in bam parsing that misprocessed low qual mutants (resolves #31)
#32
arkal
closed
6 years ago
0
Fix bug allowing low qual mutants to pass
#31
arkal
closed
6 years ago
0
handle indels
#30
arkal
closed
6 years ago
0
Filter fusion artefacts
#29
arkal
closed
6 years ago
0
Add error log for no actionable mutations (resolves #27)
#28
arkal
closed
7 years ago
0
Add error line to logfile for no actionable
#27
arkal
closed
7 years ago
0
Properly handle lack of non synonymous mutations (resolves #25)
#26
arkal
closed
7 years ago
0
Raise no actionalbe mutations if zero peptides in output
#25
arkal
closed
7 years ago
0
Skip malformed fusions (resolves #23)
#24
jpfeil
closed
7 years ago
1
Skip malformed fusion products
#23
jpfeil
closed
7 years ago
0
Add to pypi
#22
arkal
closed
6 years ago
1
Add GENCODE revisions to fusions (resolves #20)
#21
jpfeil
closed
7 years ago
2
Ensure Transgene spits out GENCODE revisions for fusions
#20
arkal
closed
7 years ago
3
Implement OxoG filtering support (resolves #13)
#19
arkal
closed
7 years ago
0
Fix snpeff n+1 issue (resolves #16)
#18
arkal
closed
7 years ago
0
Fix snpeff n+1 issue (resolves #16)
#17
arkal
closed
7 years ago
0
Fix snpeff n+1 error
#16
arkal
closed
7 years ago
0
Fix fusion alignment file error (resolves #14)
#15
jpfeil
closed
7 years ago
1
Fix missing fusion alignment file error
#14
jpfeil
closed
7 years ago
0
Add Oxo-G filtering option
#13
arkal
closed
7 years ago
0
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