标题
How to normalize metatranscriptomic count data for differential expression analysis
作者
关键词
-
出版物
PeerJ
Volume 5, Issue -, Pages e3859
出版商
PeerJ
发表日期
2017-10-17
DOI
10.7717/peerj.3859
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- 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
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