(Q36251645)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28095772%20AND%20SRC:MED&resulttype=core&format=json

10 April 2020

title

Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28095772%20AND%20SRC:MED&resulttype=core&format=json

10 April 2020

0 references

1 reference

1 reference

1 reference

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28095772%20AND%20SRC:MED&resulttype=core&format=json

10 April 2020

author name string

Alyssa Baccarella

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28095772%20AND%20SRC:MED&resulttype=core&format=json

10 April 2020

Jay Z Parrish

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28095772%20AND%20SRC:MED&resulttype=core&format=json

10 April 2020

Charles C Kim

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28095772%20AND%20SRC:MED&resulttype=core&format=json

10 April 2020

publication date

17 January 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28095772%20AND%20SRC:MED&resulttype=core&format=json

10 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28095772%20AND%20SRC:MED&resulttype=core&format=json

10 April 2020

volume

18

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28095772%20AND%20SRC:MED&resulttype=core&format=json

10 April 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28095772%20AND%20SRC:MED&resulttype=core&format=json

10 April 2020

page(s)

38

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28095772%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

10 April 2020

limma

limma

2 references

22 June 2022

https://europepmc.org/article/PMC/5240434

based on heuristic

inferred from PubMed Central ID database lookup

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

DESeq2

DESeq2

1 reference

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

edgeR

edgeR

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

1 reference

https://scigraph.springernature.com/pub.10.1186/s12859-016-1457-z

0 references

cites work

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

A benchmark for RNA-seq quantification pipelines

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

Near-optimal probabilistic RNA-seq quantification

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

Evaluation of methods for differential expression analysis on multi-group RNA-seq 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=5240434

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

Comparative assessment of methods for the computational inference of transcript isoform abundance from 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=5240434

Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

Systematically evaluating interfaces for RNA-seq analysis from a life scientist perspective

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

Malaria transmission, infection, and disease at three sites with varied transmission intensity in Uganda: implications for malaria control

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

HISAT: a fast spliced aligner with low memory requirements

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

RNA-Seq gene profiling--a systematic empirical comparison

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

HTSeq--a Python framework to work with high-throughput 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=5240434

A comparative study of techniques for differential expression analysis on 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=5240434

Comparing reference-based RNA-Seq mapping methods for non-human primate 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=5240434

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

Systematic evaluation of spliced alignment programs for 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=5240434

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

A comparison of methods 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=5240434

EBSeq: an empirical Bayes hierarchical model for inference in 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=5240434

Differential analysis of gene regulation at transcript resolution with 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=5240434

STAR: ultrafast universal RNA-seq aligner

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

Evaluation of different reference based annotation strategies using RNA-Seq - a case study in Drososphila pseudoobscura

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

Human tissues contain CD141hi cross-presenting dendritic cells with functional homology to mouse CD103+ nonlymphoid dendritic 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=5240434

Identifying differentially expressed transcripts from RNA-seq data with biological 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=5240434

The three human monocyte subsets: implications for health and disease

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

Fast gapped-read alignment with Bowtie 2

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

A comparison of statistical methods for detecting differentially expressed genes from 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=5240434

Finding consistent patterns: a nonparametric approach for identifying differential expression in 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=5240434

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

Computational methods for transcriptome annotation and quantification using 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=5240434

Full-length transcriptome assembly from RNA-Seq data without a reference genome

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

Estimation of alternative splicing isoform frequencies from 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=5240434

From RNA-seq reads to differential expression results

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

De novo assembly and 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=5240434

baySeq: empirical Bayesian methods for identifying differential expression in 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=5240434

Comparison of gene expression profiles between human and mouse monocyte subsets

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

edgeR: a Bioconductor package for differential expression analysis of digital gene expression 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=5240434

Computation for ChIP-seq and RNA-seq studies

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

Transcriptional profiling reveals developmental relationship and distinct biological functions of CD16+ and CD16- monocyte subsets

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

Statistical inferences for isoform expression in 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=5240434

SeqMap: mapping massive amount of oligonucleotides to the genome

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

Linear models and empirical bayes methods for assessing differential expression in microarray 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=5240434

Global amplification of mRNA by template-switching PCR: linearity and application to microarray 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=5240434

Significance analysis of lexical bias in 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=5240434

Significance analysis of microarrays applied to the ionizing radiation response

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

Amplification of cDNA ends based on template-switching effect and step-out PCR.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

Streaming fragment assignment for real-time analysis of sequencing experiments

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

Transcript profiling of CD16-positive monocytes reveals a unique molecular fingerprint

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

Gene expression profiling reveals the defining features of the classical, intermediate, and nonclassical human monocyte subsets.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5240434

The impact of RNA-seq aligners on gene expression estimation

22 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28095772

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Differential analysis of RNA-seq incorporating quantification uncertainty

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28095772

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/S12859-016-1457-Z

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28095772%20AND%20SRC:MED&resulttype=core&format=json

journals/bmcbi/WilliamsBPK17

10 April 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28095772%20AND%20SRC:MED&resulttype=core&format=json

10 April 2020

1 reference