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A test metric for assessing single-cell RNA-seq batch correction
scientific article published on 20 December 2018
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scholarly article
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Europe PubMed Central
PubMed publication ID
30573817
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30573817%20AND%20SRC:MED&resulttype=core&format=json
retrieved
15 April 2020
title
A test metric for assessing single-cell RNA-seq batch correction
(English)
1 reference
stated in
Europe PubMed Central
PubMed publication ID
30573817
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30573817%20AND%20SRC:MED&resulttype=core&format=json
retrieved
15 April 2020
main subject
biotechnology
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molecular biology
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RNA sequencing
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based on heuristic
inferred from title
single-cell RNA-seq
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author
Maren Büttner
series ordinal
1
1 reference
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Europe PubMed Central
PubMed publication ID
30573817
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30573817%20AND%20SRC:MED&resulttype=core&format=json
retrieved
15 April 2020
Zhichao Miao
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2
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Europe PubMed Central
PubMed publication ID
30573817
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30573817%20AND%20SRC:MED&resulttype=core&format=json
retrieved
15 April 2020
F. Alexander Wolf
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3
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Europe PubMed Central
PubMed publication ID
30573817
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30573817%20AND%20SRC:MED&resulttype=core&format=json
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15 April 2020
Sarah Teichmann
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4
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Europe PubMed Central
PubMed publication ID
30573817
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15 April 2020
Fabian J. Theis
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5
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Europe PubMed Central
PubMed publication ID
30573817
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30573817%20AND%20SRC:MED&resulttype=core&format=json
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15 April 2020
publication date
20 December 2018
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Europe PubMed Central
PubMed publication ID
30573817
reference URL
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retrieved
15 April 2020
published in
Nature Methods
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Europe PubMed Central
PubMed publication ID
30573817
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30573817%20AND%20SRC:MED&resulttype=core&format=json
retrieved
15 April 2020
volume
16
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Europe PubMed Central
PubMed publication ID
30573817
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retrieved
15 April 2020
issue
1
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Europe PubMed Central
PubMed publication ID
30573817
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30573817%20AND%20SRC:MED&resulttype=core&format=json
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15 April 2020
page(s)
43-49
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Europe PubMed Central
PubMed publication ID
30573817
reference URL
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retrieved
15 April 2020
exact match
https://scigraph.springernature.com/pub.10.1038/s41592-018-0254-1
0 references
cites work
Batch effects and the effective design of single-cell gene expression studies
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Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing
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MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data
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7 January 2021
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Missing data and technical variability in single-cell RNA-sequencing experiments
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Crossref
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7 January 2021
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Adjusting batch effects in microarray expression data using empirical Bayes methods
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7 January 2021
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Integrating single-cell transcriptomic data across different conditions, technologies, and species
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Crossref
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7 January 2021
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Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors
1 reference
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Crossref
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7 January 2021
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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
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7 January 2021
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limma powers differential expression analyses for RNA-sequencing and microarray studies
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7 January 2021
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Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.
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7 January 2021
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Accounting for technical noise in single-cell RNA-seq experiments.
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Crossref
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7 January 2021
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Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation
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7 January 2021
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Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing
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Identification of key factors conquering developmental arrest of somatic cell cloned embryos by combining embryo biopsy and single-cell sequencing
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Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos.
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Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos.
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Lineage-Specific Profiling Delineates the Emergence and Progression of Naive Pluripotency in Mammalian Embryogenesis
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Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells
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Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing
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The landscape of accessible chromatin in mammalian preimplantation embryos
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Salmon provides fast and bias-aware quantification of transcript expression
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7 January 2021
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A benchmark for RNA-seq quantification pipelines
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Crossref
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7 January 2021
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Multiplexed droplet single-cell RNA-sequencing using natural genetic variation
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Crossref
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7 January 2021
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Normalization of RNA-seq data using factor analysis of control genes or samples
1 reference
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Crossref
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https://api.crossref.org/works/10.1038%2FS41592-018-0254-1
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7 January 2021
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SCnorm: robust normalization of single-cell RNA-seq data
1 reference
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Crossref
reference URL
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7 January 2021
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A general and flexible method for signal extraction from single-cell RNA-seq data.
1 reference
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Crossref
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https://api.crossref.org/works/10.1038%2FS41592-018-0254-1
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7 January 2021
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inferred from DOI database lookup
f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.
1 reference
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Crossref
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7 January 2021
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inferred from DOI database lookup
An accurate and robust imputation method scImpute for single-cell RNA-seq data.
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Crossref
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7 January 2021
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SAVER: gene expression recovery for single-cell RNA sequencing.
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Crossref
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Recovering Gene Interactions from Single-Cell Data Using Data Diffusion
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SCANPY: large-scale single-cell gene expression data analysis.
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Crossref
reference URL
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A comparison of single-cell trajectory inference methods: towards more accurate and robust tools
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Crossref
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7 January 2021
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inferred from DOI database lookup
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Crossref
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Crossref
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Normalizing single-cell RNA sequencing data: challenges and opportunities
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Crossref
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7 January 2021
based on heuristic
inferred from DOI database lookup
Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.
1 reference
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Crossref
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7 January 2021
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inferred from DOI database lookup
Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data
1 reference
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Crossref
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The sva package for removing batch effects and other unwanted variation in high-throughput experiments
1 reference
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Crossref
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https://api.crossref.org/works/10.1038%2FS41592-018-0254-1
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7 January 2021
based on heuristic
inferred from DOI database lookup
Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses
1 reference
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Crossref
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7 January 2021
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inferred from DOI database lookup
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
1 reference
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Crossref
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https://api.crossref.org/works/10.1038%2FS41592-018-0254-1
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7 January 2021
based on heuristic
inferred from DOI database lookup
Splatter: simulation of single-cell RNA sequencing data
1 reference
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Crossref
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https://api.crossref.org/works/10.1038%2FS41592-018-0254-1
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7 January 2021
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Ensembl 2017
1 reference
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Crossref
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7 January 2021
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Erratum to: A benchmark for RNA-seq quantification pipelines.
1 reference
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COCI
reference URL
https://opencitations.net/index/coci/api/v1/references/10.1038/S41592-018-0254-1
retrieved
1 April 2022
Identifiers
DOI
10.1038/S41592-018-0254-1
1 reference
stated in
Europe PubMed Central
PubMed publication ID
30573817
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30573817%20AND%20SRC:MED&resulttype=core&format=json
retrieved
15 April 2020
Dimensions Publication ID
1110510327
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PubMed publication ID
30573817
1 reference
stated in
Europe PubMed Central
PubMed publication ID
30573817
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30573817%20AND%20SRC:MED&resulttype=core&format=json
retrieved
15 April 2020
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