Cargando…

SCnorm: robust normalization of single-cell RNA-seq data

Normalization of RNA-sequencing data is essential for accurate downstream inference, but the assumptions upon which most methods are based do not hold in the single-cell setting. Consequently, applying existing normalization methods to single-cell RNA-seq data introduces artifacts that bias downstre...

Descripción completa

Detalles Bibliográficos
Autores principales:	Bacher, Rhonda, Chu, Li-Fang, Leng, Ning, Gasch, Audrey P., Thomson, James A., Stewart, Ron M., Newton, Michael, Kendziorski, Christina
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	2017
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5473255/ https://www.ncbi.nlm.nih.gov/pubmed/28418000 http://dx.doi.org/10.1038/nmeth.4263

Ejemplares similares

Enhancing biological signals and detection rates in single-cell RNA-seq experiments with cDNA library equalization
por: Bacher, Rhonda, et al.
Publicado: (2021)

OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data
por: Leng, Ning, et al.
Publicado: (2016)

Reproducibility across single-cell RNA-seq protocols for spatial ordering analysis
por: Seirup, Morten, et al.
Publicado: (2020)

Trendy: segmented regression analysis of expression dynamics in high-throughput ordered profiling experiments
por: Bacher, Rhonda, et al.
Publicado: (2018)

A statistical approach for identifying differential distributions in single-cell RNA-seq experiments
por: Korthauer, Keegan D., et al.
Publicado: (2016)

Oscope identifies oscillatory genes in unsynchronized single cell RNA-seq experiments
por: Leng, Ning, et al.
Publicado: (2015)

Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm
por: Chu, Li-Fang, et al.
Publicado: (2016)

Design and computational analysis of single-cell RNA-sequencing experiments
por: Bacher, Rhonda, et al.
Publicado: (2016)

Normalization by distributional resampling of high throughput single-cell RNA-sequencing data
por: Brown, Jared, et al.
Publicado: (2021)

Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics
por: Barry, Christopher, et al.
Publicado: (2019)

An In Vitro Human Segmentation Clock Model Derived from Embryonic Stem Cells
por: Chu, Li-Fang, et al.
Publicado: (2019)

EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments
por: Leng, Ning, et al.
Publicado: (2015)

CHARTS: a web application for characterizing and comparing tumor subpopulations in publicly available single-cell RNA-seq data sets
por: Bernstein, Matthew N., et al.
Publicado: (2021)

Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress
por: Gasch, Audrey P., et al.
Publicado: (2017)

Quality control of single-cell RNA-seq by SinQC
por: Jiang, Peng, et al.
Publicado: (2016)

Statistical Methods for Latent Class Quantitative Trait Loci Mapping
por: Ye, Shuyun, et al.
Publicado: (2017)

MUREN: a robust and multi-reference approach of RNA-seq transcript normalization
por: Feng, Yance, et al.
Publicado: (2021)

Assessment of Single Cell RNA-Seq Normalization Methods
por: Ding, Bo, et al.
Publicado: (2017)

Robustness of single-cell RNA-seq for identifying differentially expressed genes
por: Liu, Yong, et al.
Publicado: (2023)

Robust normalization and transformation techniques for constructing gene coexpression networks from RNA-seq data
por: Johnson, Kayla A., et al.
Publicado: (2022)

Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks
por: Roy, Sushmita, et al.
Publicado: (2013)

Single Read and Paired End mRNA-Seq Illumina Libraries from 10 Nanograms Total RNA
por: Sengupta, Srikumar, et al.
Publicado: (2011)

RNA-Seq gene expression estimation with read mapping uncertainty
por: Li, Bo, et al.
Publicado: (2010)

Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema
por: Stewart, Ron, et al.
Publicado: (2013)

An Integrated Approach for RNA-seq Data Normalization
por: Yang, Shengping, et al.
Publicado: (2016)

SpatialCorr identifies gene sets with spatially varying correlation structure
por: Bernstein, Matthew N., et al.
Publicado: (2022)

An accurate and robust imputation method scImpute for single-cell RNA-seq data
por: Li, Wei Vivian, et al.
Publicado: (2018)

A robust semi-supervised NMF model for single cell RNA-seq data
por: Wu, Peng, et al.
Publicado: (2020)

A robust nonlinear low-dimensional manifold for single cell RNA-seq data
por: Verma, Archit, et al.
Publicado: (2020)

Accuracy, robustness and scalability of dimensionality reduction methods for single-cell RNA-seq analysis
por: Sun, Shiquan, et al.
Publicado: (2019)

Robust reconstruction of single-cell RNA-seq data with iterative gene weight updates
por: Sheng, Yueqi, et al.
Publicado: (2023)

Normalization Methods on Single-Cell RNA-seq Data: An Empirical Survey
por: Lytal, Nicholas, et al.
Publicado: (2020)

Non-linear Normalization for Non-UMI Single Cell RNA-Seq
por: Wu, Zhijin, et al.
Publicado: (2021)

RUV-III-NB: normalization of single cell RNA-seq data
por: Salim, Agus, et al.
Publicado: (2022)

Data-driven assessment of dimension reduction quality for single-cell omics data
por: Dong, Xiaoru, et al.
Publicado: (2022)

Robust RNA-Seq of aRNA-amplified single cell material collected by patch clamp
por: Kim, Jae Mun “Hugo”, et al.
Publicado: (2020)

Evaluation of de novo transcriptome assemblies from RNA-Seq data
por: Li, Bo, et al.
Publicado: (2014)

Robust single-cell DNA methylome profiling with snmC-seq2
por: Luo, Chongyuan, et al.
Publicado: (2018)

Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data
por: Holland, Christian H., et al.
Publicado: (2020)

Bayesian correlation is a robust gene similarity measure for single-cell RNA-seq data
por: Sanchez-Taltavull, Daniel, et al.
Publicado: (2020)

Cannot write session to /tmp/vufind_sessions/sess_kh7e05an2ahlo3765pqm4bh33d