GOATOOLS

https://www.jianshu.com/p/2620aabd4674

GO enrichment analysis:

find_enrichment.py study.txt population.txt goa_fly.gaf \
  --outfile=GO_result.txt \
  --pval=0.05  \
  --method=fdr_bh  \
  --obo=go-basic.obo \

NOTE: 当时用 .gaf 格式的 GO Annotation File 时，一定要使用 .gaf 这个 后缀

Output:

Plot the GO term tree:

go_plot.py --go_file=GO_result.txt -c -p --outfile=plot.pdf --gaf=../goa_fly2.gaf --obo=../go-basic.obo

For every GO term box:

The total number of GO terms below the GO term box is indicated by the number next to the ‘d’. Level, the minimum path from the top root term is indicated by the number next to the L. Depth, the maximum path from the top root term is indicated by the number next to the D. i: information count.

https://www.nature.com/articles/s41598-018-28948-z

PyPI: https://pypi.org/project/goatools/

GitHub: https://github.com/tanghaibao/goatools

After GO analysis, the significant GO terms can be grouped by "Section"

grouping

https://blog.csdn.net/gitblog_00001/article/details/136646379