search

kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics
BSD 3-Clause "New" or "Revised" License
7 stars 1 forks source link

cstmm R package dependency #22

Closed kfuku52 closed 3 years ago

kfuku52 commented 3 years ago

Currently, cstmm depends on these:

library(limma)
library(tidyr)
library(dplyr)

Do they all really necessary? In principle, dep packages should be minimal, and we should use base R functions instead of packages if the same process can be accomplished in a not-so-complicated way. we do need edgeR but how do we use limma-specific functions here? tidyr and dplyr speed up our exploratory data analysis, but for programs like amalgkit, they are more like so-called "technical debt" because they are not essential but increase the installation complexity.

Hego-CCTB commented 3 years ago

These were probably remnants from testing. None of these packages were actually in use. I cleaned them up in 1b3b78bb1424a2723b0ad297b017324edfc1e319