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harvardinformatics
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degenotate
MIT License
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MK test KeyError: '*'
#52
LyAndraLujan
opened
1 month ago
1
Test-data: --no-fixed-in KeyError: 'num-ingroups'
#51
periperipatus
opened
1 month ago
3
only pN pS calculated, no pvalues or direction
#50
emgiles
closed
3 months ago
15
How to extract 0-fold and 4-fold sites from VCF files, based on the output of degenotate
#49
xiadawei123
closed
3 months ago
3
Extract Conserved 4D sites from alignment
#48
simone-says
closed
4 months ago
5
Update README.md
#47
osipovarev
closed
7 months ago
0
Update README.md
#46
osipovarev
closed
7 months ago
0
added imputed maf cutoff as an argument
#45
osipovarev
closed
9 months ago
0
imputed MKT extension
#44
osipovarev
closed
9 months ago
1
Fix bug when GFF info field has trailing semi-colon
#43
gwct
closed
1 year ago
0
Fix CDS processing issue
#42
tsackton
closed
1 year ago
0
empty bed and .tsv file
#41
rezenman
closed
1 year ago
3
fixed missing return value in getVariants
#40
gwct
closed
1 year ago
0
Index out of range
#39
aguilar-gomez
closed
1 year ago
6
updating readme
#38
gwct
closed
1 year ago
0
updating the develop branch to match main
#37
gwct
closed
1 year ago
0
just updating the version string
#36
gwct
closed
1 year ago
0
added -maf and --no-fixed-in options
#35
gwct
closed
1 year ago
0
Added warnings for various transcript issues
#34
gwct
closed
1 year ago
0
Error GXF1: Invalid number of IDs found during transcript parent id parsing AND Error GXF2: No CDS exons found in input annotation file! Cannot calculate degeneracy without coding sequences
#33
milesroberts-123
closed
1 year ago
6
ValueError issue
#32
LeebanY
closed
1 year ago
3
added check for .csi vcf index in addition to .tbi
#31
gwct
closed
1 year ago
0
**Error SEQ2: Some exons have differing strands
#30
lisagrigoreva
closed
1 year ago
7
Allow csi index for vcf files
#29
tsackton
closed
1 year ago
1
Negative strand variant bug
#28
gwct
closed
1 year ago
0
added -m option
#27
gwct
closed
1 year ago
0
Fixed bugs related to invariant/missing sites in VCF files
#26
gwct
closed
1 year ago
0
Minor bug fixes
#25
gwct
closed
1 year ago
0
Fix issues related to 0 length transcripts
#24
gwct
closed
1 year ago
0
Degenotate doesn't run, returning KeyError
#23
rancilhac
closed
1 year ago
14
Add MK test functionality and options to write amino acid sequences
#22
gwct
closed
1 year ago
0
ModuleNotFoundError: No module named 'degenotate_lib'
#21
milesroberts-123
closed
1 year ago
10
README and other minor things
#20
gwct
closed
1 year ago
0
moving recipe files that got copied erroneously
#19
gwct
closed
1 year ago
0
moved lib/ to degenotate_lib/ for bioconda recipe
#18
gwct
closed
1 year ago
0
Fix bugs, efficiency improvements
#17
tsackton
closed
1 year ago
0
Mismatch between fasta chromosome names and gff chromosome names
#16
milesroberts-123
closed
1 year ago
4
Automatically replace ambiguous bases with N
#15
milesroberts-123
closed
1 year ago
4
Getting starting frame from GXF files
#14
tsackton
closed
1 year ago
0
Fix errors in frame calculations
#13
tsackton
closed
1 year ago
0
Develop
#12
tsackton
closed
1 year ago
0
Transcript output and misc
#11
gwct
closed
1 year ago
0
Version 0.1 alpha
#10
tsackton
closed
2 years ago
0
More test data, direct CDS input
#9
gwct
closed
2 years ago
0
test data
#8
gwct
closed
2 years ago
0
test data and refining gxf parsing code
#7
gwct
closed
2 years ago
0
Test data
#6
tsackton
closed
2 years ago
2
Initial output code
#5
gwct
closed
2 years ago
0
Reduce redundant code when reading GXF files
#4
gwct
closed
2 years ago
1
Reading CDS from individual files
#3
gwct
closed
2 years ago
1
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