RNA-Seq optimization with eQTL gold standards (Q30564266)

20 August 2017

RNA-Seq optimization with eQTL gold standards (English)

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20 August 2017

1 reference

1 reference

5

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24341889%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Shannon Ellis

1

1 reference

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11 June 2020

author name string

Simone Gupta

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24341889%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Foram N Ashar

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24341889%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Joel S Bader

4

1 reference

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11 June 2020

Dan E Arking

6

1 reference

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11 June 2020

language of work or name

English

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publication date

17 December 2013

1 reference

20 August 2017

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11 June 2020

volume

14

1 reference

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11 June 2020

page(s)

892

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Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

11 June 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

Normalizing RNA-sequencing data by modeling hidden covariates with prior knowledge

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

Association between SNPs and gene expression in multiple regions of the human brain

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

Brain expression genome-wide association study (eGWAS) identifies human disease-associated variants

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

A beginner's guide to eukaryotic genome annotation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

Genotype imputation with thousands of genomes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

Removing technical variability in RNA-seq data using conditional quantile normalization

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

GC-content normalization for RNA-Seq data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

seeQTL: a searchable database for human eQTLs

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

Computational methods for transcriptome annotation and quantification using RNA-seq

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

The architecture of gene regulatory variation across multiple human tissues: the MuTHER study

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

Tackling the widespread and critical impact of batch effects in high-throughput data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

Quality control for genome-wide association studies

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

Bioinformatics challenges for genome-wide association studies

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

The Sequence Alignment/Map format and SAMtools

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

TopHat: discovering splice junctions with RNA-Seq

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

Evaluating the performance of Affymetrix SNP Array 6.0 platform with 400 Japanese individuals

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

Capturing heterogeneity in gene expression studies by surrogate variable analysis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

PLINK: a tool set for whole-genome association and population-based linkage analyses

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

GenABEL: an R library for genome-wide association analysis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

Microarray data analysis: from disarray to consolidation and consensus

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

Statistical significance for genomewide studies

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

Genomic control for association studies

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890578

The beginning of the end for microarrays?

14 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-14-892

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-14-892

The Genotype-Tissue Expression (GTEx) project

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-14-892

Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-14-892

21 January 2018

Identifiers

DOI

10.1186/1471-2164-14-892

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24341889%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

11 June 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24341889%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

PubMed publication ID

24341889

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24341889%20AND%20SRC:MED&resulttype=core&format=json