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Rename
fgsea
function togsea
, and modify:method
parameter: default is "gseapy"; alternatively support "fgsea"gseapy.prerank
function, and rename columns in resulting data frame to match fgsea, so thatplot_gsea
function andwrite_gsea_results_to_excel
function can work properlyde_key
andlog2fc_key
torank_key
, which takes"de_key:attr_key"
format so that users don't need to specify 2 parametersn_jobs=4
by defaultverbose
parameter for GSEAPy methodpadj
values in ascending order, then by absolute values ofNES
scores in descending order, and then bypathway
names in dictionary orderRename
write_fgsea_results_to_excel
towrite_gsea_results_to_excel