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Co-expression network analysis software tools | RNA sequencing data

RNA-seq co-expression analysis is in its infancy and reasonable practices remain poorly defined.

Source text:
(Ballouz et al., 2015) Guidance for RNA-seq co-expression network construction and analysis: safety in numbers. Bioinformatics.

G T A T C G C T A
EPIG-Seq
Desktop

EPIG-Seq

Allows identification of co-expressed genes from RNA-Seq data (EPIG-Seq).…

Allows identification of co-expressed genes from RNA-Seq data (EPIG-Seq). EPIG-Seq permits users to estimate dispersion in the data and identify statistically significant clusters of co-expressed…

G T A T C G C T A
RNAMiner
Web

RNAMiner

A multi-level bioinformatics protocol and pipeline. RNAMiner includes five…

A multi-level bioinformatics protocol and pipeline. RNAMiner includes five steps: Mapping RNA-Seq reads to a reference genome, calculating gene expression values, identifying differentially expressed…

G T A T C G C T A
AMOUNTAIN
Desktop

AMOUNTAIN

Aims to search active modules in multi-layer WGCN using a continuous…

Aims to search active modules in multi-layer WGCN using a continuous optimization approach. AMOUNTAIN is a fine grained method to identify active modules on the multi-layer weighted (co-expression…

G T A T C G C T A
TRAP
Desktop
Web

TRAP Time-series RNA-seq Analysis Package

A comprehensive package integrating all necessary tasks such as mapping short…

A comprehensive package integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis…

G T A T C G C T A
RNA-seq…
Dataset

RNA-seq networks

A variety of RNA-seq expression data were assessed to determine factors…

A variety of RNA-seq expression data were assessed to determine factors affecting functional connectivity and topology in co-expression networks. RNA-seq networks are available as a resource for…

AMEN
Desktop

AMEN Annotation Mapping Expression and Network

Enables biological and medical researchers with basic bioinformatics training…

Enables biological and medical researchers with basic bioinformatics training to manage and explore genome annotation, chromosomal mapping, protein -protein interaction (PPI), expression profiling…

Information

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