Evaluation of logistic regression models and effect of covariates for case-control study in RNA-Seq analysis (Q36271926)

13 August 2017

Evaluation of logistic regression models and effect of covariates for case-control study in RNA-Seq analysis (English)

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logistic regression model

13 August 2017

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Kathryn L Lunetta

4

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Josée Dupuis

Josée Dupuis

5

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Adam Labadorf

Adam T Labadorf

2

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author name string

Seung Hoan Choi

1

1 reference

13 August 2017

Richard H Myers

3

1 reference

13 August 2017

Anita L DeStefano

6

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13 August 2017

6 February 2017

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13 August 2017

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13 August 2017

18

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13 August 2017

1

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13 August 2017

91

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describes a project that uses

13 August 2017

DESeq2

DESeq2

DESeq

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

limma

limma

1 reference

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

exact match

https://scigraph.springernature.com/pub.10.1186/s12859-017-1498-y

0 references

cites work

RNA Sequence Analysis of Human Huntington Disease Brain Reveals an Extensive Increase in Inflammatory and Developmental Gene Expression

1 reference

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Evaluation of methods for differential expression analysis on multi-group RNA-seq count data

30 September 2017

1 reference

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

30 September 2017

1 reference

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Association of Brain DNA methylation in SORL1, ABCA7, HLA-DRB5, SLC24A4, and BIN1 with pathological diagnosis of Alzheimer disease

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5294900

Building a pipeline to discover and validate novel therapeutic targets and lead compounds for Alzheimer's disease

30 September 2017

1 reference

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

30 September 2017

1 reference

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Dispersion estimation and its effect on test performance in RNA-seq data analysis: a simulation-based comparison of methods

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5294900

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

30 September 2017

1 reference

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TCC: an R package for comparing tag count data with robust normalization strategies

30 September 2017

1 reference

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5294900

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments

30 September 2017

1 reference

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5294900

Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors.

30 September 2017

1 reference

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A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

30 September 2017

1 reference

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Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data

30 September 2017

1 reference

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Normalization, testing, and false discovery rate estimation for RNA-sequencing data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5294900

Differential expression in RNA-seq: a matter of depth

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5294900

Identification of SPOCK2 as a susceptibility gene for bronchopulmonary dysplasia

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5294900

Differential expression analysis for sequence count data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5294900

baySeq: empirical Bayesian methods for identifying differential expression in sequence count data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5294900

A data-adaptive sum test for disease association with multiple common or rare variants

30 September 2017

1 reference

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

30 September 2017

1 reference

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Identification of novel tumor markers in prostate, colon and breast cancer by unbiased methylation profiling

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5294900

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5294900

Genomic control for association studies

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5294900

Molecular cloning of testican-2: defining a novel calcium-binding proteoglycan family expressed in brain

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5294900

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5294900

Striatal excitatory amino acid transporter transcript expression in schizophrenia, bipolar disorder, and major depressive disorder

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5294900

PEP-19 immunohistochemistry defines the basal ganglia and associated structures in the adult human brain, and is dramatically reduced in Huntington's disease

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5294900

Permutation P-values should never be zero: calculating exact P-values when permutations are randomly drawn.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5294900

A solution to the problem of separation in logistic regression.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5294900

Cellular and synaptic localization of the neuronal glutamate transporters excitatory amino acid transporter 3 and 4.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5294900

The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq

22 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2FS12859-017-1498-Y

10.1186/S12859-017-1498-Y

21 January 2018

Identifiers

DOI

1 reference

journals/bmcbi/ChoiLMLDD17

13 August 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

13 August 2017

1 reference