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。The effect of tissue composition on gene co-expression
Yun Zhang et al.
BRIEFINGS IN BIOINFORMATICS (2021)
DataRemix: a universal data transformation for optimal inference from gene expression datasets
Weiguang Mao et al.
BIOINFORMATICS (2021)
Single-cell co-expression analysis reveals that transcriptional modules are shared across cell types in the brain
Benjamin D. Harris et al.
CELL SYSTEMS (2021)
Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols
Shanrong Zhao et al.
RNA (2020)
Untangling the effects of cellular composition on coexpression analysis
Marjan Farahbod et al.
GENOME RESEARCH (2020)
Differential coexpression in human tissues and the confounding effect of mean expression levels
Marjan Farahbod et al.
BIOINFORMATICS (2019)
A systematic evaluation of single cell RNA-seq analysis pipelines
Beate Vieth et al.
NATURE COMMUNICATIONS (2019)
Addressing confounding artifacts in reconstruction of gene co-expression networks
Princy Parsana et al.
GENOME BIOLOGY (2019)
TISSUES 2.0: an integrative web resource on mammalian tissue expression
Oana Palasca et al.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2018)
wTO: an R package for computing weighted topological overlap and a consensus network with integrated visualization tool
Deisy Morselli Gysi et al.
BMC BIOINFORMATICS (2018)
Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions
Ciaran Evans et al.
BRIEFINGS IN BIOINFORMATICS (2018)
Reproducible RNA-seq analysis using recount2
Leonardo Collado-Torres et al.
NATURE BIOTECHNOLOGY (2017)
Exploiting single-cell expression to characterize co-expression replicability
Megan Crow et al.
GENOME BIOLOGY (2016)
Guidance for RNA-seq co-expression network construction and analysis: safety in numbers
S. Ballouz et al.
BIOINFORMATICS (2015)
Understanding multicellular function and disease with human tissue-specific networks
Casey S. Greene et al.
NATURE GENETICS (2015)
Targeted exploration and analysis of large cross-platform human transcriptomic compendia
Qian Zhu et al.
NATURE METHODS (2015)
The Impact of Normalization Methods on RNA-Seq Data Analysis
J. Zyprych-Walczak et al.
BIOMED RESEARCH INTERNATIONAL (2015)
quantro: a data-driven approach to guide the choice of an appropriate normalization method
Stephanie C. Hicks et al.
GENOME BIOLOGY (2015)
The Precision-Recall Plot Is More Informative than the ROC Plot When Evaluating Binary Classifiers on Imbalanced Datasets
Takaya Saito et al.
PLOS ONE (2015)
Normalization of RNA-seq data using factor analysis of control genes or samples
Davide Risso et al.
NATURE BIOTECHNOLOGY (2014)
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Michael I. Love et al.
GENOME BIOLOGY (2014)
A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
Marie-Agnes Dillies et al.
BRIEFINGS IN BIOINFORMATICS (2013)
The Genotype-Tissue Expression (GTEx) project
John Lonsdale et al.
NATURE GENETICS (2013)
mRNA enrichment protocols determine the quantification characteristics of external RNA spike-in controls in RNA-Seq studies
Qing Tao et al.
SCIENCE CHINA-LIFE SCIENCES (2013)
Affymetrix GeneChip microarray preprocessing for multivariate analyses
Matthew N. McCall et al.
BRIEFINGS IN BIOINFORMATICS (2012)
Unsupervised pattern discovery in human chromatin structure through genomic segmentation
Michael M. Hoffman et al.
NATURE METHODS (2012)
Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples
Gunter P. Wagner et al.
THEORY IN BIOSCIENCES (2012)
Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling
Pawel P. Labaj et al.
BIOINFORMATICS (2011)
Computational methods for transcriptome annotation and quantification using RNA-seq
Manuel Garber et al.
NATURE METHODS (2011)
The Sequence Read Archive
Rasko Leinonen et al.
NUCLEIC ACIDS RESEARCH (2011)
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
Mark D. Robinson et al.
BIOINFORMATICS (2010)
On the Choice and Number of Microarrays for Transcriptional Regulatory Network Inference
Elissa J. Cosgrove et al.
BMC BIOINFORMATICS (2010)
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
James H. Bullard et al.
BMC BIOINFORMATICS (2010)
A scaling normalization method for differential expression analysis of RNA-seq data
Mark D. Robinson et al.
GENOME BIOLOGY (2010)
Differential expression analysis for sequence count data
Simon Anders et al.
GENOME BIOLOGY (2010)
Transcript length bias in RNA-seq data confounds systems biology
Alicia Oshlack et al.
BIOLOGY DIRECT (2009)
Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain
Katja Nowick et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data
Daniel Ramskold et al.
PLOS COMPUTATIONAL BIOLOGY (2009)
The Sleipnir library for computational functional genomics
Curtis Huttenhower et al.
BIOINFORMATICS (2008)
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Ali Mortazavi et al.
NATURE METHODS (2008)
Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks
Wei Keat Lim et al.
BIOINFORMATICS (2007)
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
Jeremiah J. Faith et al.
PLOS BIOLOGY (2007)
Finding function: evaluation methods for functional genomic data
Chad L. Myers et al.
BMC GENOMICS (2006)
Validation of alternative methods of data normalization in gene co-expression studies
A Reverter et al.
BIOINFORMATICS (2005)
A general framework for weighted gene co-expression network analysis
Bin Zhang et al.
STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY (2005)
Quantifying the relationship between co-expression, co-regulation and gene function
DJ Allocco et al.
BMC BIOINFORMATICS (2004)
Systematic genome-wide screens of gene function
AE Carpenter et al.
NATURE REVIEWS GENETICS (2004)
A module map showing conditional activity of expression modules in cancer
E Segal et al.
NATURE GENETICS (2004)
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
BM Bolstad et al.
BIOINFORMATICS (2003)
分享论文
