How to normalize metatranscriptomic count data for differential expression analysis

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

SAMSA: a comprehensive metatranscriptome analysis pipeline

(2016) Samuel T. Westreich et al.   BMC BIOINFORMATICS

Comparison of normalization and differential expression analyses using RNA-Seq data from 726 individual Drosophila melanogaster

(2016) Yanzhu Lin et al.   BMC GENOMICS

Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate

(2016) Francesca De Filippis et al.   Scientific Reports

MetaTrans: an open-source pipeline for metatranscriptomics

(2016) Xavier Martinez et al.   Scientific Reports

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis

(2015) Yuzhen Ye et al.   BIOINFORMATICS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests

(2015) Cedar N. Hesse et al.   Frontiers in Microbiology

compcodeR--an R package for benchmarking differential expression methods for RNA-seq data

(2014) C. Soneson   BIOINFORMATICS

Land Use Type Significantly Affects Microbial Gene Transcription in Soil

(2014) Heiko Nacke et al.   MICROBIAL ECOLOGY

Relating the metatranscriptome and metagenome of the human gut

(2014) E. A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation

(2014) Albi Celaj et al.   Microbiome

A comparison of methods for differential expression analysis of RNA-seq data

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome

(2013) Nathan P. McNulty et al.   PLOS BIOLOGY

Comparative meta-RNA-seq of the vaginal microbiota and differential expression by Lactobacillus iners in health and dysbiosis

(2013) Jean M Macklaim et al.   Microbiome

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill

(2012) Olivia U Mason et al.   ISME Journal

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data

(2011) Jun Li et al.   STATISTICAL METHODS IN MEDICAL RESEARCH

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

Polymorphic Cis- and Trans-Regulation of Human Gene Expression

(2010) Vivian G. Cheung et al.   PLOS BIOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Achievements and new knowledge unraveled by metagenomic approaches

(2009) Carola Simon et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre

(2009) Rachel S. Poretsky et al.   ENVIRONMENTAL MICROBIOLOGY

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome

(2008) Tim Urich et al.   PLoS One

Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities

(2008) Jack A. Gilbert et al.   PLoS One

Microbial community gene expression in ocean surface waters

(2008) J. Frias-Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA