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Gene expression clustering software tools | RNA sequencing data analysis

RNA-seq technology has been widely adopted as an attractive alternative to microarray-based methods to study global gene expression. However, robust statistical tools to analyze these complex datasets are still lacking. By grouping genes with…
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AltAnalyze
Desktop

AltAnalyze

An easy-to-use application for microarray, RNA-Seq and metabolomics analysis.…

An easy-to-use application for microarray, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), AltAnalyze will assess…

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MBCluster.Seq
Desktop

MBCluster.Seq

Cluster genes based on Poisson or Negative-Binomial model for RNA-Seq or other…

Cluster genes based on Poisson or Negative-Binomial model for RNA-Seq or other digital gene expression (DGE) data. Results from both simulation studies and analysis of a maize RNA-seq dataset show…

QUBIC
Desktop

QUBIC QUery BICluster

Implements a well-cited biclustering algorithm, QUBIC, for the interpretation…

Implements a well-cited biclustering algorithm, QUBIC, for the interpretation of gene expression profile data. The unique features of QUBIC include: (i) biclustering is integrated with analyses…

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ctsGE
Desktop

ctsGE

Allows to visualize and explore the gene-expression patterns and their…

Allows to visualize and explore the gene-expression patterns and their subclusters. ctsGE proposes a way to organize and explore expression data without eliminating valuable information. It divides…

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coseq
Desktop

coseq Co-Expression Analysis of Sequencing Data

Facilitates implementation and visualization of the recommended RNA-seq…

Facilitates implementation and visualization of the recommended RNA-seq co-expression analyses. coseq implements Gaussian and Poisson mixture models to cluster gene expression profiles from…

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optCluster
Desktop

optCluster

Allows to proceed different cluster analyses. optCluster provides a solution…

Allows to proceed different cluster analyses. optCluster provides a solution (both clustering algorithm and number of clusters) using a single function. It enables users to evaluate various…

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CountClust
Desktop

CountClust

Allows users to fit Grade of membership models (GoM) for clustering of RNA-seq…

Allows users to fit Grade of membership models (GoM) for clustering of RNA-seq gene expression count data. CountClust also provides tools to identify which genes are most distinctively expressed in…

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HTSCluster
Desktop

HTSCluster

Implements a Poisson mixture model to cluster observations (e.g., genes) in…

Implements a Poisson mixture model to cluster observations (e.g., genes) in high throughput sequencing data. Parameter estimation is performed using either the EM or CEM algorithm, and the slope…

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DGEclust
Desktop

DGEclust

A program for clustering and differential expression analysis of expression…

A program for clustering and differential expression analysis of expression data generated by next-generation sequencing assays, such as RNA-seq, CAGE and others. DGEclust takes as input a table of…

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Zika-RNAseq-Pip…
Desktop

Zika-RNAseq-Pipeline

Provides an open source RNA-seq processing pipeline that can be used to extract…

Provides an open source RNA-seq processing pipeline that can be used to extract knowledge from any study that profiled gene expression using RNA-seq applied to mammalian cells, comparing two…

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RapClust
Desktop

RapClust

A fast and accurate methodology for clustering contigs from de novo…

A fast and accurate methodology for clustering contigs from de novo transcriptome assemblies based upon the relationships exposed by multi-mapping sequencing fragments. RapClust, implements recent…

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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…

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rsgcc
Desktop

rsgcc

Infers regulatory relationships of genes from transcriptomic data. rsgcc is…

Infers regulatory relationships of genes from transcriptomic data. rsgcc is based on the Gini correlation method to proceed. It is able to calculate associations between two genes based on…

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LSTrAP
Desktop

LSTrAP Large-Scale Transcriptome Analysis Pipeline

Pre-processes RNA-seq data and maps it to the genome. LSTrAP performs quality…

Pre-processes RNA-seq data and maps it to the genome. LSTrAP performs quality control and produces co-expression networks. It provides functional and comparative genomics data to enable a host of…

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necklace
Desktop

necklace

Automatically combines transcriptomes from difference sources, such as assembly…

Automatically combines transcriptomes from difference sources, such as assembly and annotation, into a compact and unified reference. necklace is applicable to any species with an incomplete…

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ECC
Desktop

ECC Entropy-based Consensus Clustering

Performs entropy-based consensus clustering. ECC (Entropy-based Consensus…

Performs entropy-based consensus clustering. ECC (Entropy-based Consensus Clustering) is a clustering algorithm for patient stratification. ECC method employs an entropy-based utility function to…

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Bio CorEx
Desktop

Bio CorEx Correlation Explanation

Recovers latent factors with Correlation Explanation (CorEx). Bio CorEx…

Recovers latent factors with Correlation Explanation (CorEx). Bio CorEx consists of python code to build these representations. The principle of Total CorEx has recently been introduced as a way to…

CD-HIT
Desktop
Web

CD-HIT

A widely used program for clustering biological sequences to reduce sequence…

A widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. In response to the rapid increase in the amount of…

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AMAP
Desktop

AMAP Another Multidimensional Analysis Package

Provides a set of methods for clustering and analysis. AMAP is a R package that…

Provides a set of methods for clustering and analysis. AMAP is a R package that contains approaches for standard hierarchical clustering and k-means. The software also permits users to apply several…

LAS
Desktop

LAS Large Average Submatrices

Finds large average submatrices within a given real-valued data matrix. LAS…

Finds large average submatrices within a given real-valued data matrix. LAS operates in an iterative-residual fashion, and is driven by a Bonferroni-based significance score that effectively trades…

DeBi
Desktop

DeBi Differentially Expressed Biclusters

Discovers maximum size homogeneous biclusters in which each gene is strongly…

Discovers maximum size homogeneous biclusters in which each gene is strongly associated with a subset of samples. DeBi is based on a well known data mining approach called frequent item set. The…

BiBit
Desktop

BiBit

Extracts Bit-Patterns from binary datasets. BiBit will apply a cumulative…

Extracts Bit-Patterns from binary datasets. BiBit will apply a cumulative binarization process and will generate 11 different versions of the same dataset. The Bibit algorithm source code is…

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