j-andrews7 VAMPIRE issues

j-andrews7 / 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
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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