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Reduce dependencies #143

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bschilder opened this issue Feb 16, 2023 · 0 comments
Open
6 tasks

Reduce dependencies #143

bschilder opened this issue Feb 16, 2023 · 0 comments
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@serachoi1230
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enhancement New feature or request

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@bschilder
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EpiCompare currently has >200 dependencies (direct + indirect deps)! This is partly due to the fact that it aims to be a comprehensive pipeline, but there are some things that can ameliorate this.

Candidate packages to remove:

  • reshape2: data.table can handle all of this functionality.
  • tidyr: data.table can handle all of this functionality.
  • plyranges: Only used once in EpiCompare::write_example_peaks
  • Matrix: Only used once in EpiCompare::rebin_peaks
  • BiocParallel or parallel: We should pick one and stick with it (probably BiocParallel since it's recommended by Bioc)
  • scales: Only used in EpiCompare:::compute_percentiles. Can't probably implement in base R.
@bschilder bschilder added the enhancement New feature or request label Feb 16, 2023
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@bschilder @serachoi1230