(Q41152743)

27 September 2017

Splatter: simulation of single-cell RNA sequencing data (English)

1 reference

27 September 2017

0 references

3

1 reference

27 September 2017

Luke Zappia

1

0 references

Belinda Phipson

Belinda Phipson

series ordinal

2

0 references

publication date

12 September 2017

1 reference

27 September 2017

1 reference

27 September 2017

18

1 reference

27 September 2017

1

1 reference

27 September 2017

174

1 reference

describes a project that uses

27 September 2017

ggplot2

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&rettype=xml&id=5596896

ggplot2

2 references

10 June 2022

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

edgeR

edgeR

edgeR package

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

DESeq2

DESeq

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

tximport

tximport

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Gene length and detection bias in single cell RNA sequencing protocols

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

SC3: consensus clustering of single-cell RNA-seq data

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

Salmon provides fast and bias-aware quantification of transcript expression

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

Batch effects and the effective design of single-cell gene expression studies

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

A statistical approach for identifying differential distributions in single-cell RNA-seq experiments

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

Coming of age: ten years of next-generation sequencing technologies

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

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

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

Innate-like functions of natural killer T cell subsets result from highly divergent gene programs

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

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

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

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

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

Human cerebral organoids recapitulate gene expression programs of fetal neocortex development

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

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

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

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

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

Spatial reconstruction of single-cell gene expression data

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

Orchestrating high-throughput genomic analysis with Bioconductor

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

voom: Precision weights unlock linear model analysis tools for RNA-seq read counts

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

STAR: ultrafast universal RNA-seq aligner

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

Bpipe: a tool for running and managing bioinformatics pipelines

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

Counting absolute numbers of molecules using unique molecular identifiers

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

RNA sequencing: advances, challenges and opportunities

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

Differential expression analysis for sequence count data

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

mRNA-Seq whole-transcriptome analysis of a single cell

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

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

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

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

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5596896

Ancient DNA and the rewriting of human history: be sparing with Occam's razor

14 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2FS13059-017-1305-0

An accurate and robust imputation method scImpute for single-cell RNA-seq data.

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28899397

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A general and flexible method for signal extraction from single-cell RNA-seq data.

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28899397

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

SAVER: gene expression recovery for single-cell RNA sequencing.

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28899397

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/S13059-017-1305-0

1 reference

Dimensions Publication ID

27 September 2017

0 references

1 reference

27 September 2017

PubMed publication ID

28899397

1 reference