Code

Simplify handling of motif files#6

Code

Merged

nictru merged 25 commits intodevnf-core/tfactivity:devfrom motif-filesnf-core/tfactivity:motif-filesCopy head branch name to clipboardMay 30, 2024

+682-645

Commits

Commits on Apr 29, 2024

• Simplify ROSE script

  nictru

  committed
  123821f

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• Use bed file directly in ROSE

  nictru

  committed
  9874e1f

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• Use standard genepred file in ROSE

  nictru

  committed
  ae028dc

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• Remove traces of UCSC parameter

  nictru

  committed
  c7d3bb7

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• Remove refseq traces from ROSE script

  nictru

  committed
  06c77a2

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• Fix GTF channel structure for ROSE

  nictru

  committed
  c4d2dac

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• Remove unnecessary igenomes values

  nictru

  committed
  b811dd1

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• Add CONVERT_MOTIFS process

  nictru

  committed
  723ad2b

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• Remove duplicate taxon id

  nictru

  committed
  2a284df

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• Implement motif subworkflow

  nictru

  committed
  704e9a9

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• Implement first version of psem creation

  nictru

  committed
  481d75f

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• Use template in TRANSFAC_TO_PSEM

  nictru

  committed
  0c92f44

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• Fix TRANSFAC_TO_PSEM environment

  nictru

  committed
  3758c3b

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• Improve TRANSFAC_TO_PSEM performannce

  nictru

  committed
  2600722

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• Fix PSEM compatibility problems

  nictru

  committed
  64096ab

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• Remove PWM filtering in peaks subworkflow

  nictru

  committed
  d761ba4

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• Implement motif filtering in Motif subworkflow

  nictru

  committed
  90cf274

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• Implement motif version capture

  nictru

  committed
  bb3fd58

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• Implement jaspar motif fetching

  nictru

  committed
  e9ef113

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• Convert TF names to uppercase in JASPAR fetching

  nictru

  committed
  ce42260

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• Editorconfig

  nictru

  committed
  dc8691d

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• Editorconfig + Linting

  nictru

  committed
  761c1a5

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Commits on May 18, 2024

• Integrated MOTIFS output into FIMO

  LeonHafner

  committed
  8aa6b93

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Commits on May 27, 2024

• switched from pwm to meme file

  LeonHafner

  committed
  600cce2

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Commits on May 30, 2024

• integrated JASPAR_MAPPING into FILTER_MOTIFS

  LeonHafner

  committed
  2656f79

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