j-andrews7/VAMPIRE

Issues

• Position of variant within motif.

  #46 opened 7 years ago
  0

• summarize.py bugs, tests, & refactors

  #44 opened 8 years ago
  0

• Many motif databases provide PFMs rather than count matrices

  #42 opened 8 years ago
  0

• TF name/gene symbol discordance

  #41 opened 8 years ago
  1

• 'join' used as method name in motif.py

  #40 opened 8 years ago
  2

• motifs.py output order right investigation

  #39 opened 8 years ago
  8

• gene_expression.py bugs, tests & refactors

  #38 opened 8 years ago
  0

• variant code duplication

  #37 opened 8 years ago
  2

• tf_expression: bed file format

  #36 opened 8 years ago
  1

• get_motifs length all not individual TF

  #35 opened 8 years ago
  2

• activity.py bugs, tests & refactors

  #34 opened 8 years ago
  2

• thresholds.py bugs, tests, and refactors

  #33 opened 8 years ago
  0

• tf_expression.py bugs, tests & refactors

  #32 opened 8 years ago
  0

• motifs.py bugs, tests & refactors

  #31 opened 8 years ago
  3

• Other motif scanning/comparison tools.

  #30 opened 8 years ago
  0

• control and documented runs

  #29 opened 8 years ago
  2

• Motif clustering as a potential feature.

  #28 opened 8 years ago
  0

• Allow iterative or parallel processing for ChIP-seq data.

  #27 opened 8 years ago
  1

• Handle multiple motifs for same TF.

  #26 opened 8 years ago
  1

• Print command to header.

  #25 opened 8 years ago
  0

• tf_expression.py motif INFO fields order is off.

  #24 opened 8 years ago
  1

• Bed output for motifs.py may be incorrect.

  #23 opened 8 years ago
  1

• Sequence longer than PWM bug.

  #22 opened 8 years ago
  3

• Check if motifs.py works with sorted VCFs.

  #21 opened 8 years ago
  1

• Better handling of compound variants.

  #19 opened 8 years ago
  0

• Write check to get sample names from VCF header.

  #18 opened 8 years ago
  1

• Validate VCF output after each step.

  #17 opened 8 years ago
  1

• Change annotation format to use VAMP as INFO field.

  #16 opened 8 years ago
  0

• Change format from single VCFs to multi-sample VCF instead.

  #15 opened 8 years ago
  2

• Reference homotypic matches aren't output currently.

  #14 opened 8 years ago
  1

• Convert to Google-style docstrings for consistency.

  #13 opened 8 years ago
  1

• Implement VCF output for enhancer activity command.

  #12 opened 8 years ago
  2

• Add flexibility for gene identification when checking gene expression.

  #11 opened 8 years ago
  0

• Use consistent format for motif databases.

  #10 opened 8 years ago
  3

• Add additional motif databases.

  #9 opened 8 years ago
  0

• Set up documentation pages.

  #8 opened 8 years ago
  0

• Include ENCODE data files.

  #7 opened 8 years ago
  1

• Add data files as necessary.

  #6 opened 8 years ago
  0

• Add gene expression checking.

  #5 opened 8 years ago
  1

• Remove OptionsList use.

  #4 opened 8 years ago
  3

• Remove extraneous documention.

  #3 opened 8 years ago
  1

• Change all current scripts to modules.

  #2 opened 8 years ago
  0

• Remove numpy dependence.

  #1 opened 8 years ago
  0