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.
EpiComparecurrently 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.tablecan handle all of this functionality.tidyr:data.tablecan handle all of this functionality.plyranges: Only used once inEpiCompare::write_example_peaksMatrix: Only used once inEpiCompare::rebin_peaksBiocParallelorparallel: We should pick one and stick with it (probablyBiocParallelsince it's recommended by Bioc)scales: Only used inEpiCompare:::compute_percentiles. Can't probably implement in base R.