Guidance for RNA-seq co-expression network construction and analysis: safety in numbers (Q42608562)

3 November 2017

Guidance for RNA-seq co-expression network construction and analysis: safety in numbers (English)

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3 November 2017

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J Gillis

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author name string

S Ballouz

series ordinal

1

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PubMed ID

25717192

3 November 2017

W Verleyen

series ordinal

2

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PubMed ID

25717192

3 November 2017

language of work or name

English

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publication date

24 February 2015

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3 November 2017

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3 November 2017

31

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3 November 2017

2123-2130

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3 November 2017

13

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Gene ontology: tool for the unification of biology

3 November 2017

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

Statistical design and analysis of RNA sequencing data

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

Identifying Important Risk Factors for Survival in Kidney Graft Failure Patients Using Random Survival Forests

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

Reactome: a database of reactions, pathways and biological processes

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

Cluster analysis and display of genome-wide expression patterns

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

The impact of multifunctional genes on "guilt by association" analysis

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

The role of indirect connections in gene networks in predicting function

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

GENCODE: the reference human genome annotation for The ENCODE Project

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

Genes, behavior and next-generation RNA sequencing.

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

Utilizing RNA-Seq data for de novo coexpression network inference

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

KEGG: kyoto encyclopedia of genes and genomes

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

Fast gapped-read alignment with Bowtie 2

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

Coexpression analysis of human genes across many microarray data sets

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

The sequence read archive

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

Detecting and correcting systematic variation in large-scale RNA sequencing data

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

RNA-seq differential expression studies: more sequence or more replication?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

Mapping and quantifying mammalian transcriptomes by RNA-Seq

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

The Structure and Function of Complex Networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

parmigene--a parallel R package for mutual information estimation and gene network reconstruction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

Measuring the wisdom of the crowds in network-based gene function inference.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

Transcriptomic analysis of autistic brain reveals convergent molecular pathology

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

Guilt-by-association goes global

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV118

10.1093/BIOINFORMATICS/BTV118

21 January 2018

Identifiers

DOI

1 reference

journals/bioinformatics/BallouzVG15

3 November 2017

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DBLP Dataset 2021-01-02

28 January 2021

1 reference

PubMed ID

25717192