Metagenomic biomarker discovery and explanation
Citations
7,032 citations
3,060 citations
2,791 citations
2,507 citations
Cites background or methods from "Metagenomic biomarker discovery and..."
..., 2012), and (3) Galaxy platform-based LDA Effect Size analysis (LEfSe; Segata et al., 2011)....
[...]
...…(1) Metastats comparison (White et al., 2009) and (2) Random Forests algorithm, under QIIME (Knights et al., 2011) or coupled with Boruta feature selection, in the Genboree microbiome toolset (Riehle et al., 2012), and (3) Galaxy platform-based LDA Effect Size analysis (LEfSe; Segata et al., 2011)....
[...]
2,189 citations
References
23,312 citations
"Metagenomic biomarker discovery and..." refers methods in this paper
...LEfSe is implemented in Python and makes use of R statistical functions in the coin [111] and MASS [112] libraries through the rpy2 library [113] and of the matplotlib [114] library for graphical output....
[...]
18,346 citations
17,446 citations
17,350 citations
"Metagenomic biomarker discovery and..." refers methods in this paper
...UniFrac [38] compares sets of metagenomes at a strictly taxonomic level using phylogenetic distance, while MGRAST [39], ShotgunFunctionalizeR [40], mothur [41], and METAREP [42] all process metagenomic data using standard statistical tests (mainly t-tests with some modifications)....
[...]
...Resulting sequences were processed using a data curation pipeline implemented in mothur [41], which reduces the sequencing error rate to less than 0....
[...]
16,048 citations
"Metagenomic biomarker discovery and..." refers methods in this paper
...Except as stated otherwise, taxonomic abundances for 16S samples were generated from filtered sequence reads using the RDP classifier [101], with confidences below 80% rebinned to ‘uncertain’....
[...]