(Q36371785)

29 September 2017

Normalizing single-cell RNA sequencing data: challenges and opportunities (English)

1 reference

29 September 2017

1 reference

5

1 reference

29 September 2017

Catalina A Vallejos

1

0 references

Antonio Scialdone

object named as

Antonio Scialdone

series ordinal

3

0 references

Davide Risso

object named as

Davide Risso

series ordinal

2

0 references

Sandrine Dudoit

series ordinal

4

object named as

Sandrine Dudoit

1 reference

PMC publication ID

5549838

29 September 2017

language of work or name

1 reference

15 May 2017

1 reference

29 September 2017

1 reference

29 September 2017

14

1 reference

29 September 2017

6

1 reference

29 September 2017

565-571

1 reference

https://scigraph.springernature.com/pub.10.1038/nmeth.4292

29 September 2017

0 references

cites work

Single-cell mRNA quantification and differential analysis with Census

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Beyond comparisons of means: understanding changes in gene expression at the single-cell level

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Design and computational analysis of single-cell RNA-sequencing experiments

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Single-cell genome sequencing: current state of the science

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Design and Analysis of Single-Cell Sequencing Experiments

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Computational assignment of cell-cycle stage from single-cell transcriptome data

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

The technology and biology of single-cell RNA sequencing

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Computational and analytical challenges in single-cell transcriptomics

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

svaseq: removing batch effects and other unwanted noise from sequencing data

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Normalization of RNA-seq data using factor analysis of control genes or samples

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Single-cell RNA-seq: advances and future challenges

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Bayesian approach to single-cell differential expression analysis

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Quantitative single-cell RNA-seq with unique molecular identifiers

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Single-cell sequencing-based technologies will revolutionize whole-organism science

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Revisiting global gene expression analysis

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Synthetic spike-in standards for RNA-seq experiments

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Differential expression analysis for sequence count data

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

A scaling normalization method for differential expression analysis of RNA-seq data

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

mRNA-Seq whole-transcriptome analysis of a single cell

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Mapping and quantifying mammalian transcriptomes by RNA-Seq

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Normalization of cDNA microarray data

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Spliced synthetic genes as internal controls in RNA sequencing experiments

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Normalization and noise reduction for single cell RNA-seq experiments

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Accounting for technical noise in single-cell RNA-seq experiments.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

RNA-Seq gene expression estimation with read mapping uncertainty

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

Diffusion pseudotime robustly reconstructs lineage branching

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5549838

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

21 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNMETH.4292

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1038/NMETH.4292

1 reference

29 September 2017

1 reference

PMC publication ID

5549838

29 September 2017

PubMed publication ID

28504683

1 reference

PMC publication ID

5549838