NGS data analysis

Question

[Sanjai S]

Which is the best Ballgown or DEseq2?

Answer 1

[noodle]

Based on github pages, it looks like Ballgown is abandoned.

https://github.com/alyssafrazee/ballgown

https://github.com/mikelove/DESeq2

Also, the bioconductor stats are quite telling;

https://www.bioconductor.org/packages/stats/bioc/DESeq2/

https://www.bioconductor.org/packages/stats/bioc/ballgown/