(Q36020652)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27190234%20AND%20SRC:MED&resulttype=core&format=json

1 April 2020

title

RNAontheBENCH: computational and empirical resources for benchmarking RNAseq quantification and differential expression methods (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27190234%20AND%20SRC:MED&resulttype=core&format=json

1 April 2020

1 reference

computational benchmark

1 reference

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27190234%20AND%20SRC:MED&resulttype=core&format=json

1 April 2020

Alessandro Vitriolo

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27190234%20AND%20SRC:MED&resulttype=core&format=json

1 April 2020

Antonio Adamo

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27190234%20AND%20SRC:MED&resulttype=core&format=json

1 April 2020

Vivek Das

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27190234%20AND%20SRC:MED&resulttype=core&format=json

1 April 2020

Giuseppe Testa

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27190234%20AND%20SRC:MED&resulttype=core&format=json

1 April 2020

author name string

Pasquale Laise

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27190234%20AND%20SRC:MED&resulttype=core&format=json

1 April 2020

language of work or name

English

0 references

publication date

17 May 2016

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27190234%20AND%20SRC:MED&resulttype=core&format=json

1 April 2020

published in

Nucleic Acids Research

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27190234%20AND%20SRC:MED&resulttype=core&format=json

1 April 2020

volume

44

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27190234%20AND%20SRC:MED&resulttype=core&format=json

1 April 2020

issue

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27190234%20AND%20SRC:MED&resulttype=core&format=json

1 April 2020

page(s)

5054-5067

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27190234%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution-NonCommercial 4.0 International

1 April 2020

copyright license

start time

11 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

A benchmark for RNA-seq quantification pipelines

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

Do count-based differential expression methods perform poorly when genes are expressed in only one condition?

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

Errors in RNA-Seq quantification affect genes of relevance to human disease

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

Polyester: simulating RNA-seq datasets with differential transcript expression

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

HISAT: a fast spliced aligner with low memory requirements

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

limma powers differential expression analyses for RNA-sequencing and microarray studies

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

HTSeq--a Python framework to work with high-throughput sequencing data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

Systematic evaluation of spliced alignment programs for RNA-seq data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

A comparison of methods for differential expression analysis of RNA-seq data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

Differential analysis of gene regulation at transcript resolution with RNA-seq

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

STAR: ultrafast universal RNA-seq aligner

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

Differential expression analysis for sequence count data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

The Sequence Alignment/Map format and SAMtools

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

RNA-Seq: a revolutionary tool for transcriptomics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

Direct multiplexed measurement of gene expression with color-coded probe pairs

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

Evaluation of external RNA controls for the assessment of microarray performance

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

7q11.23 dosage-dependent dysregulation in human pluripotent stem cells affects transcriptional programs in disease-relevant lineages

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

Comparison of software packages for detecting differential expression in RNA-seq studies

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

RNA-Seq gene expression estimation with read mapping uncertainty

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

Comparison of Affymetrix GeneChip expression measures.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4914128

Mojo Hand, a TALEN design tool for genome editing applications.

23 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKW448

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

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKW448

Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKW448

Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage.

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27190234

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKW448

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27190234%20AND%20SRC:MED&resulttype=core&format=json

1 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27190234%20AND%20SRC:MED&resulttype=core&format=json

1 April 2020

PubMed publication ID

27190234

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27190234%20AND%20SRC:MED&resulttype=core&format=json