Table 1 The characteristics of existing packages for biomarker detection. Y: Yes, N: No, CL: Command Line

Boruta [15]

-R

-CL

-R frame

N

N

N

N

Y

edgeR [23]

-R

-CL

-R frame

N

N

-Filtering

Y

N

-Normalization

DESeq2 [24]

-R

-CL

-R frame

N

N

N

N

N

ENNB [16]

-R

-CL

-R frame

N

N

-Normalization

N

N

MetagenomeSeq [17]

-R

-CL

- R frame

N

N

-Normalization

N

N

MicrobiomeDDA [18]

-R

-CL

-R frame

N

N

-Normalization

N

N

Shotgun- FunctionalizeR [19]

-R

-CL

- R frame

N

N

N

N

Y

MetaStats [20]

-R

-CL

-R frame

N

N

-Normalization

N

N

Raida [21]

-R

-CL

-R frame

N

N

N

N

N

LEfSe [9]

-Python

-CL -Web

-Tabular

Y

Y

N

N

N

MetaML [13]

-Python

-CL

-tsv

N

N

N

Y

N

Fizzy [14]

-Python

-CL

-biom -csv

N

N

N

N

N

“stats” package of R [30]

-R

-CL

-R frame

N

N

N

N

N

FANTOM\(^*\) [22]

-Python

-GUI

-txt

NA

N

N

N

N

STAMP [31]

-Python

-GUI

-tsv

N

N

-Filtering

N

N

XIPE-TOTEC [32]

-Python

-CL -Web

-tsv

N

N

N

N

N

Microbiome Analyst [33]

-Java Script

-Web

-txt -csv -biom

N

N

-Filtering -Scaling -Normalization -Transformation

Y

N

-Java

-R

METAREP [27]

-Python -Java -Matlab

-CL -GUI

-txt -xlsx -mat

N

N

N

Y

N

DAME [34]

-R

-Web

-biom -csv -trf -HDF5 -JSON

N

Y

-Filtering

Y

N

ShinyMB [35]

-R

-Web

-csv -tsv

N

N

-Stratification

Y

N

MetaFS [28]

-Web server

-Web

-csv

N

N

-Centering -Transformation -Scaling -Normalization

Y

N

RPCA\(^*\) [10]

-Matlab -C

-CL

-xls

N

N

N

N

N

RegLRSD [11]

-Matlab -C

-GUI

-xls

N

N

N

N

N

MetaAnalyst

-Matlab

-GUI

-csv -tsv -xls -mat -biom -json

Y

Y

-Scaling -Normalization -Centering

Y

Y