Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data

Wang Q(2007)Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy Appl Env Microbiol 73 5261-5267

Garrity GM(2015)MetaPhlAn2 for enhanced metagenomic taxonomic profiling Nat Methods 12 902-903

Tiedje JM(2017)Advances in single-cell RNA sequencing and its applications in cancer research Oncotarget. 8 53763-53779

Cole JR(2016)Revealing the vectors of cellular identity with single-cell genomics Nat Biotechnol 34 1145-1160

Truong DT(2018)Single-cell RNA sequencing to explore immune cell heterogeneity Nat Rev Immunol 18 35-45

Franzosa EA(2015)Computational and analytical challenges in single-cell transcriptomics Nat Rev Genet 16 133-145

Tickle TL(2014)Bayesian approach to single-cell differential expression analysis Nat Methods 11 740-742

Scholz M(2017)Normalization and microbial differential abundance strategies depend upon data characteristics Microbiome. 5 27-1202

Weingart G(2016)Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies Microbiome. 4 62-140

Pasolli E(2013)Differential abundance analysis for microbial marker-gene surveys Nat Methods 10 1200-420

Wang Q(2007)Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy Appl Env Microbiol 73 5261-5267

Garrity GM(2015)MetaPhlAn2 for enhanced metagenomic taxonomic profiling Nat Methods 12 902-903

Tiedje JM(2017)Advances in single-cell RNA sequencing and its applications in cancer research Oncotarget. 8 53763-53779

Cole JR(2016)Revealing the vectors of cellular identity with single-cell genomics Nat Biotechnol 34 1145-1160

Truong DT(2018)Single-cell RNA sequencing to explore immune cell heterogeneity Nat Rev Immunol 18 35-45

Franzosa EA(2015)Computational and analytical challenges in single-cell transcriptomics Nat Rev Genet 16 133-145

Tickle TL(2014)Bayesian approach to single-cell differential expression analysis Nat Methods 11 740-742

Scholz M(2017)Normalization and microbial differential abundance strategies depend upon data characteristics Microbiome. 5 27-1202

Weingart G(2016)Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies Microbiome. 4 62-140

Pasolli E(2013)Differential abundance analysis for microbial marker-gene surveys Nat Methods 10 1200-420