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uclahs-cds
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package-moPepGen
Multi-Omics Peptide Generator
https://uclahs-cds.github.io/package-moPepGen/
GNU General Public License v2.0
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Coordinate of Noncaonincal Peptide
#833
zhuchcn
closed
8 months ago
6
Czhu fix summarize fasta
#832
zhuchcn
closed
11 months ago
4
Fix brute force to shift insertion to end inclusion for noncoding transcripts
#831
zhuchcn
closed
11 months ago
0
Enable using index files without checking for versions
#830
zhuchcn
closed
11 months ago
2
In-bubble reference node treated as subgraph-in mistakenly
#829
zhuchcn
closed
12 months ago
0
Fix summarizeFasta that summarize table keys not determined correctly with source comb in --order-source
#828
zhuchcn
closed
1 year ago
0
summarizeFasta error with combination sources
#827
lydiayliu
closed
1 year ago
1
Fix PVG that downstream node skipped mistakenly after cleaving
#826
zhuchcn
closed
1 year ago
0
Test case added to confirm that source combinations of more than 2 in --order-source is handled
#825
zhuchcn
closed
1 year ago
1
VariantSourceSet Comparison Fixed
#824
zhuchcn
closed
1 year ago
1
Update splitFasta and summarizeFasta to accept source combinations in --order-source
#823
zhuchcn
closed
1 year ago
0
Additional testing of merged MNVs
#822
lydiayliu
opened
1 year ago
0
Alternative Way to Handle Trypsin Exception
#821
zhuchcn
opened
1 year ago
0
Autofix broken Confluence links
#820
nwiltsie
closed
1 year ago
0
Unconsistency between splitFasta and summarizeFasta
#819
zhuchcn
opened
1 year ago
1
Complex validation for index files
#818
zhuchcn
closed
9 months ago
0
Fix MNV and generateIndex
#817
zhuchcn
closed
1 year ago
3
Version bump to 1.2.1
#816
zhuchcn
closed
1 year ago
1
Added fuzz test log reseults
#815
zhuchcn
closed
1 year ago
3
Fix issues raised by fuzz test
#814
zhuchcn
closed
1 year ago
0
Fuzz test fixes
#813
zhuchcn
closed
1 year ago
0
Fix callVariant and bruteForce from fuzz test
#812
zhuchcn
closed
1 year ago
1
Some more peculiarities with `summarizeFasta`
#811
lydiayliu
closed
1 year ago
5
BruteForce ignores accepter variants if the donor TX has a variant with the same corodinate
#810
zhuchcn
closed
1 year ago
0
Fix splitFasta & summarizeFasta to handle ALT+Noncoding
#809
zhuchcn
closed
1 year ago
2
Fix splitFasta to use top priority fasta header in additional split
#808
zhuchcn
closed
1 year ago
0
Source group gets override by GVF order in splitFasta
#807
zhuchcn
closed
1 year ago
0
Support ordering source groups directly in splitFasta
#806
zhuchcn
closed
1 year ago
0
splitFasta source group order got override by GVF order
#805
zhuchcn
closed
1 year ago
0
Fix callVariant with altSplice and intronic frameshift very close to the end of the subgraph
#804
zhuchcn
closed
1 year ago
0
AltSplice insertion with another frameshift variant closed to the end of the subgraph end
#803
zhuchcn
closed
1 year ago
0
Variant alignment failed with an SNV in altSplice insertion and another SNV right after it
#802
zhuchcn
closed
1 year ago
1
Fix callVariant
#801
zhuchcn
closed
1 year ago
0
Cleavage lost missing in downstream node
#800
zhuchcn
closed
1 year ago
0
Fix callVariant with in-frame subgraphs
#799
zhuchcn
closed
1 year ago
2
Add support for --group-source in summarizeFasta
#798
zhuchcn
closed
1 year ago
0
Group CodonReassign and SECT in splitFasta
#797
zhuchcn
closed
1 year ago
1
`splitFasta` cannot group AltTranslation peptides
#796
lydiayliu
closed
1 year ago
1
`summarizeFasta` takes a lot of time?
#795
lydiayliu
closed
1 year ago
3
Fix callVariant when `call_peptides_main` does not return graph data
#794
zhuchcn
closed
1 year ago
0
Deletion from start codon to exon end
#793
zhuchcn
closed
1 year ago
0
Fuzz test & Fix callVariant
#792
zhuchcn
closed
1 year ago
2
Fix `summarizeFasta` that SEC and W2F not counted with fusion
#791
zhuchcn
closed
1 year ago
0
Save graph data
#790
zhuchcn
closed
1 year ago
1
`W2F` when part of Fusion is not counted as separate variant?
#789
lydiayliu
closed
1 year ago
3
doc (moPepGen): version bump to 1.2.0
#788
zhuchcn
closed
1 year ago
0
fix (callVariant): Fixed callVariant that `fit_into_codon` terminated…
#787
zhuchcn
closed
1 year ago
0
Fusion with frameshift in donor and variant right after accepter breakpoint
#786
zhuchcn
closed
1 year ago
0
Fuzz test history
#785
zhuchcn
closed
1 year ago
5
circRNA node last fragment not checked if it's hybrid
#784
zhuchcn
closed
1 year ago
2
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