Library dplyr

 # filter() (and slice())

 # filter based on text match
 filter(mydata, Danio_symbol=="hoxd4a" )

 # filter based on regular expression match
 filter(mydata, grepl("hox", Danio_symbol) )

 # filter based on columns above or below levels
 filter(mydata, main.EO > 20000, Sach.s.EO > 20000, Hunter.s.EO> 20000, sk..muscle< 100 )

 # filter based on ratio of columns
 filter(mydata, Sach.s.EO/sk..muscle > 50)
 filter(mydata, Sach.s.EO/sk..muscle > 50, sk..muscle > 10)

 # arrange()

 # select() (and rename())

 # distinct()


 # mutate() (and transmute())

 # summarise()

 # sample_n() (and sample_frac())