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j-andrews7
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VAMPIRE
Variant and Epigenetic anNotation for Underlying Significance and Regulation
MIT License
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Position of variant within motif.
#46
j-andrews7
opened
7 years ago
0
Experimental
#45
j-andrews7
closed
7 years ago
0
summarize.py bugs, tests, & refactors
#44
j-andrews7
opened
7 years ago
0
Dev
#43
j-andrews7
closed
7 years ago
0
Many motif databases provide PFMs rather than count matrices
#42
j-andrews7
opened
7 years ago
0
TF name/gene symbol discordance
#41
j-andrews7
opened
7 years ago
1
'join' used as method name in motif.py
#40
j-andrews7
closed
7 years ago
2
motifs.py output order right investigation
#39
Crumbs350
opened
7 years ago
8
gene_expression.py bugs, tests & refactors
#38
j-andrews7
opened
7 years ago
0
variant code duplication
#37
Crumbs350
opened
7 years ago
2
tf_expression: bed file format
#36
Crumbs350
closed
7 years ago
1
get_motifs length all not individual TF
#35
Crumbs350
closed
7 years ago
2
activity.py bugs, tests & refactors
#34
j-andrews7
opened
7 years ago
2
thresholds.py bugs, tests, and refactors
#33
j-andrews7
opened
7 years ago
0
tf_expression.py bugs, tests & refactors
#32
j-andrews7
opened
7 years ago
0
motifs.py bugs, tests & refactors
#31
j-andrews7
opened
7 years ago
3
Other motif scanning/comparison tools.
#30
j-andrews7
opened
7 years ago
0
control and documented runs
#29
Crumbs350
opened
7 years ago
2
Motif clustering as a potential feature.
#28
j-andrews7
opened
7 years ago
0
Allow iterative or parallel processing for ChIP-seq data.
#27
j-andrews7
closed
7 years ago
1
Handle multiple motifs for same TF.
#26
j-andrews7
closed
7 years ago
1
Print command to header.
#25
j-andrews7
opened
7 years ago
0
tf_expression.py motif INFO fields order is off.
#24
j-andrews7
closed
7 years ago
1
Bed output for motifs.py may be incorrect.
#23
j-andrews7
closed
7 years ago
1
Sequence longer than PWM bug.
#22
j-andrews7
closed
7 years ago
3
Check if motifs.py works with sorted VCFs.
#21
j-andrews7
closed
7 years ago
1
Dev
#20
j-andrews7
closed
8 years ago
0
Better handling of compound variants.
#19
j-andrews7
opened
8 years ago
0
Write check to get sample names from VCF header.
#18
j-andrews7
opened
8 years ago
1
Validate VCF output after each step.
#17
j-andrews7
closed
7 years ago
1
Change annotation format to use VAMP as INFO field.
#16
j-andrews7
opened
8 years ago
0
Change format from single VCFs to multi-sample VCF instead.
#15
j-andrews7
closed
8 years ago
2
Reference homotypic matches aren't output currently.
#14
j-andrews7
closed
7 years ago
1
Convert to Google-style docstrings for consistency.
#13
j-andrews7
opened
8 years ago
1
Implement VCF output for enhancer activity command.
#12
j-andrews7
closed
8 years ago
2
Add flexibility for gene identification when checking gene expression.
#11
j-andrews7
opened
8 years ago
0
Use consistent format for motif databases.
#10
j-andrews7
closed
7 years ago
3
Add additional motif databases.
#9
j-andrews7
opened
8 years ago
0
Set up documentation pages.
#8
j-andrews7
opened
8 years ago
0
Include ENCODE data files.
#7
j-andrews7
opened
8 years ago
1
Add data files as necessary.
#6
j-andrews7
opened
8 years ago
0
Add gene expression checking.
#5
j-andrews7
closed
7 years ago
1
Remove OptionsList use.
#4
j-andrews7
closed
7 years ago
3
Remove extraneous documention.
#3
j-andrews7
closed
7 years ago
1
Change all current scripts to modules.
#2
j-andrews7
closed
7 years ago
0
Remove numpy dependence.
#1
j-andrews7
closed
8 years ago
0