Cargando…

RNA-Seq differential expression analysis: An extended review and a software tool

The correct identification of differentially expressed genes (DEGs) between specific conditions is a key in the understanding phenotypic variation. High-throughput transcriptome sequencing (RNA-Seq) has become the main option for these studies. Thus, the number of methods and softwares for different...

Descripción completa

Detalles Bibliográficos
Autores principales:	Costa-Silva, Juliana, Domingues, Douglas, Lopes, Fabricio Martins
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Public Library of Science 2017
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5739479/ https://www.ncbi.nlm.nih.gov/pubmed/29267363 http://dx.doi.org/10.1371/journal.pone.0190152

Ejemplares similares

Temporal progress of gene expression analysis with RNA-Seq data: A review on the relationship between computational methods
por: Costa-Silva, Juliana, et al.
Publicado: (2022)

Comparison of software packages for detecting differential expression in RNA-seq studies
por: Seyednasrollah, Fatemeh, et al.
Publicado: (2015)

Differential Expression Analysis for RNA-Seq: An Overview of Statistical Methods and Computational Software
por: Huang, Huei-Chung, et al.
Publicado: (2015)

MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps
por: Khomtchouk, Bohdan B., et al.
Publicado: (2016)

FusionFinder: A Software Tool to Identify Expressed Gene Fusion Candidates from RNA-Seq Data
por: Francis, Richard W., et al.
Publicado: (2012)

Differential Expression Analysis for RNA-Seq Data
por: Gupta, Rashi, et al.
Publicado: (2012)

TRANSIT - A Software Tool for Himar1 TnSeq Analysis
por: DeJesus, Michael A., et al.
Publicado: (2015)

A survey of software for genome-wide discovery of differential splicing in RNA-Seq data
por: Hooper, Joan E
Publicado: (2014)

3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists
por: Guo, Wenbin, et al.
Publicado: (2020)

Systematic evaluation of differential splicing tools for RNA-seq studies
por: Mehmood, Arfa, et al.
Publicado: (2019)

Differential expression analysis for paired RNA-seq data
por: Chung, Lisa M, et al.
Publicado: (2013)

Power analysis for RNA-Seq differential expression studies
por: Yu, Lianbo, et al.
Publicado: (2017)

Robustness of differential gene expression analysis of RNA-seq
por: Stupnikov, A., et al.
Publicado: (2021)

S-MART, A Software Toolbox to Aid RNA-seq Data Analysis
por: Zytnicki, Matthias, et al.
Publicado: (2011)

P482: ACCUFUSION: A HIGHLY SCALABLE SOFTWARE TOOL FOR DETECTING GENE FUSIONS BY RNA-SEQ IN LEUKEMIA
por: Su, Xiaoping, et al.
Publicado: (2023)

Novel Data Transformations for RNA-seq Differential Expression Analysis
por: Zhang, Zeyu, et al.
Publicado: (2019)

Stability of methods for differential expression analysis of RNA-seq data
por: Lin, Bingqing, et al.
Publicado: (2019)

A survey of statistical software for analysing RNA-seq data
por: Gao, Dexiang, et al.
Publicado: (2010)

On Differential Gene Expression Using RNA-Seq Data
por: Lee, Juhee, et al.
Publicado: (2011)

From RNA-seq reads to differential expression results
por: Oshlack, Alicia, et al.
Publicado: (2010)

The impact of amplification on differential expression analyses by RNA-seq
por: Parekh, Swati, et al.
Publicado: (2016)

Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods
por: Quinn, Thomas P., et al.
Publicado: (2018)

Limitations of alignment-free tools in total RNA-seq quantification
por: Wu, Douglas C., et al.
Publicado: (2018)

Discrete distributional differential expression (D(3)E) - a tool for gene expression analysis of single-cell RNA-seq data
por: Delmans, Mihails, et al.
Publicado: (2016)

A comparison of methods for differential expression analysis of RNA-seq data
por: Soneson, Charlotte, et al.
Publicado: (2013)

Differential expression analysis of RNA-seq data at single-base resolution
por: Frazee, Alyssa C., et al.
Publicado: (2014)

Power analysis and sample size estimation for RNA-Seq differential expression
por: Ching, Travers, et al.
Publicado: (2014)

RNA-Seq workflow: gene-level exploratory analysis and differential expression
por: Love, Michael I., et al.
Publicado: (2015)

Best practices on the differential expression analysis of multi-species RNA-seq
por: Chung, Matthew, et al.
Publicado: (2021)

Impact of human gene annotations on RNA-seq differential expression analysis
por: Hamaguchi, Yu, et al.
Publicado: (2021)

Integrative Differential Expression Analysis for Multiple EXperiments (IDEAMEX): A Web Server Tool for Integrated RNA-Seq Data Analysis
por: Jiménez-Jacinto, Verónica, et al.
Publicado: (2019)

scDIOR: single cell RNA-seq data IO software
por: Feng, Huijian, et al.
Publicado: (2022)

Sensitivity, specificity, and reproducibility of RNA-Seq differential expression calls
por: Łabaj, Paweł P., et al.
Publicado: (2016)

Finding differentially expressed sRNA-Seq regions with srnadiff
por: Zytnicki, Matthias, et al.
Publicado: (2021)

ARH-seq: identification of differential splicing in RNA-seq data
por: Rasche, Axel, et al.
Publicado: (2014)

How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?
por: Schurch, Nicholas J., et al.
Publicado: (2016)

An evaluation of RNA-seq differential analysis methods
por: Li, Dongmei, et al.
Publicado: (2022)

Transcriptionally active LTR retrotransposons in Eucalyptus genus are differentially expressed and insertionally polymorphic
por: Marcon, Helena Sanches, et al.
Publicado: (2015)

MetaRNA-Seq: An Interactive Tool to Browse and Annotate Metadata from RNA-Seq Studies
por: Kumar, Pankaj, et al.
Publicado: (2015)

DELongSeq for efficient detection of differential isoform expression from long-read RNA-seq data
por: Hu, Yu, et al.
Publicado: (2023)

Cannot write session to /tmp/vufind_sessions/sess_arqp4rnu8ieo1dtshk9frh3lua