Bayesian Hierarchical Model for Differential Gene Expression Using RNA-Seq Data
暂无分享,去创建一个
Peter Müller | Yuan Ji | Juhee Lee | Guoshuai Cai | Shoudan Liang | P. Müller | Yuan Ji | S. Liang | Juhee Lee | G. Cai | S. Liang
[1] Gabor T. Marth,et al. Whole-genome sequencing and variant discovery in C. elegans , 2008, Nature Methods.
[2] Hongkai Ji,et al. Analyzing 'omics data using hierarchical models , 2010, Nature Biotechnology.
[3]
R. Durbin,et al.
Mapping Quality Scores Mapping Short Dna Sequencing Reads and Calling Variants Using P ,
2022
.
[4]
B. Williams,et al.
Mapping and quantifying mammalian transcriptomes by RNA-Seq
,
2008,
Nature Methods.
[5]
W. Huber,et al.
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets
,
2011
.
[6]
Deepayan Sarkar,et al.
Detecting differential gene expression with a semiparametric hierarchical mixture method.
,
2004,
Biostatistics.
[7]
W. Wong,et al.
Modeling non-uniformity in short-read rates in RNA-Seq data
,
2010,
Genome Biology.
[8]
P. Müller,et al.
Optimal Sample Size for Multiple Testing
,
2004
.
[9]
C. Robert,et al.
A Mixture Approach to Bayesian Goodness of Fit
,
2002
.
[10]
Peter Müller,et al.
On Differential Gene Expression Using RNA-Seq Data
,
2011,
Cancer informatics.
[11]
Zhijin Wu,et al.
Empirical bayes analysis of sequencing-based transcriptional profiling without replicates
,
2010,
BMC Bioinformatics.
[12]
M. Robinson,et al.
A scaling normalization method for differential expression analysis of RNA-seq data
,
2010,
Genome Biology.
[13]
John D. Storey,et al.
Empirical Bayes Analysis of a Microarray Experiment
,
2001
.
[14]
Nicholas T. Ingolia,et al.
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
,
2009,
Science.
[15]
Michael Brudno,et al.
SHRiMP: Accurate Mapping of Short Color-space Reads
,
2009,
PLoS Comput. Biol..
[16]
R. Doerge,et al.
Statistical Design and Analysis of RNA Sequencing Data
,
2010,
Genetics.
[17]
M. Stephens,et al.
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays.
,
2008,
Genome research.
[18]
Xuegong Zhang,et al.
DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
,
2010,
Bioinform..
[19]
Mark D. Robinson,et al.
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
,
2009,
Bioinform..
[20]
A. Oshlack,et al.
Transcript length bias in RNA-seq data confounds systems biology
,
2009,
Biology Direct.
[21]
Patrick M. Tarwater,et al.
Codon choice in genes depends on flanking sequence information—implications for theoretical reverse translation
,
2008,
Nucleic acids research.
[22]
Ruiqiang Li,et al.
SOAP: short oligonucleotide alignment program
,
2008,
Bioinform..
[23]
Mark D. Robinson,et al.
Moderated statistical tests for assessing differences in tag abundance
,
2007,
Bioinform..
[24]
Cole Trapnell,et al.
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
,
2009,
Genome Biology.
[25]
Piotr J. Balwierz,et al.
Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data
,
2009,
Genome Biology.
[26]
K. Hansen,et al.
Biases in Illumina transcriptome sequencing caused by random hexamer priming
,
2010,
Nucleic acids research.
[27]
Catalin C. Barbacioru,et al.
mRNA-Seq whole-transcriptome analysis of a single cell
,
2009,
Nature Methods.
[28]
Matthew D. Young,et al.
From RNA-seq reads to differential expression results
,
2010,
Genome Biology.
[29]
Sandrine Dudoit,et al.
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
,
2010,
BMC Bioinformatics.
[30]
James O. Berger,et al.
Ockham's Razor and Bayesian Analysis
,
1992
.
[31]
Li Deng,et al.
Overdispersed logistic regression for SAGE: Modelling multiple groups and covariates
,
2004,
BMC Bioinformatics.
[32]
Schraga Schwartz,et al.
Detection and Removal of Biases in the Analysis of Next-Generation Sequencing Reads
,
2011,
PloS one.
[33]
Thomas J. Hardcastle,et al.
baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data
,
2010,
BMC Bioinformatics.
[34]
Stefan Schwarz,et al.
A Field Guide to Pandemic, Epidemic and Sporadic Clones of Methicillin-Resistant Staphylococcus aureus
,
2011,
PloS one.
[35]
Juliane C. Dohm,et al.
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
,
2008,
Nucleic acids research.