network analysis SPIEC-EASI code?

mibwurrepo / Microbial-bioinformatics-introductory-course-Material-2018

Course material for OPEN & REPRODUCIBLE MICROBIOME DATA ANALYSIS SPRING SCHOOL

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network analysis SPIEC-EASI code? #10

Closed marwa38 closed 2 years ago

marwa38 commented 2 years ago

Hello

Thanks very much for sharing this course workflow for analysing microbiome studies. Is there any possibility to let me know how to work with SPIEC-EASI code used for network analysis after deprecating some parts of the function? net.c <- spiec.easi(otu.c, method='mb', icov.select.params=list(rep.num=50))

Many Thanks Marwa

microsud commented 2 years ago

Hi Marwa! Unfortunately I have not used the latest version of SPIEC-EASI tool. May be the latest documentation of the pkg https://github.com/zdk123/SpiecEasi has relevant guidelines.