Pros: from SummarizedExperiment to tidybulk you jusy need one command %>% tidybulk(). Everything is automatic. We save so much data wrangling (many lines of joining, reshaping, etc.. ) and we can use that time to explain something more interesting.
Temporary cons: the column count is now counts. I will correct it in dev soon
Temporary possible cons: the key column is now ENSEMBL ID not gene. So the analysis is done at ENSEMBL ID level. This will be solvable with a small edits in the development of tidybulk. But someone can argue that having it at ENSEMBL ID and knowing the matching GENE ID for plotting would be even better. Nonetheless, we will be able to choose our transcript column anyway, so this issue will become irrelevant.
Pros: from SummarizedExperiment to tidybulk you jusy need one command %>% tidybulk(). Everything is automatic. We save so much data wrangling (many lines of joining, reshaping, etc.. ) and we can use that time to explain something more interesting.
Temporary cons: the column
countis nowcounts. I will correct it in dev soonTemporary possible cons: the key column is now ENSEMBL ID not gene. So the analysis is done at ENSEMBL ID level. This will be solvable with a small edits in the development of tidybulk. But someone can argue that having it at ENSEMBL ID and knowing the matching GENE ID for plotting would be even better. Nonetheless, we will be able to choose our transcript column anyway, so this issue will become irrelevant.