The analysis of gene expression from time series underpins many biological studies. Two basic forms of analysis recur for data of this type: removing inactive (quiet) genes from the study and determining which genes are differentially expressed. Often these analysis stages are…
STEM
Desktop

STEM Short Time-series Expression Miner

A software program specifically designed for the analysis of short time series…

A software program specifically designed for the analysis of short time series microarray gene expression data. STEM implements unique methods to cluster, compare, and visualize such data. STEM also…

maSigPro
Desktop

maSigPro

A package specifically suited for the analysis of time-course gene expression…

A package specifically suited for the analysis of time-course gene expression data, which was developed originally for microarrays and hence was limited in its application to count data. Updated…

CYCLE
Desktop

CYCLE

Package for assessing the statistical significance of periodic expression based…

Package for assessing the statistical significance of periodic expression based on Fourier analysis and comparison with data generated by different background models.

G T A T C G C T A
ImpulseDE
Desktop

ImpulseDE

Captures single impulse-like progression patterns in high throughput time…

Captures single impulse-like progression patterns in high throughput time series datasets. ImpulseDE can be applied on any kind of high throughput gene expression data. It reports differentially…

TTCA
Desktop

TTCA Transcript Time Course Analysis

Analyses sparse and heterogeneous time course data with high detection…

Analyses sparse and heterogeneous time course data with high detection sensitivity and transparency. TTCA is specifically designed for the analysis of perturbation responses. It combines different…

Mfuzz
Desktop

Mfuzz

Package for noise-robust soft clustering of gene expression time-series data…

Package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface).

gprege
Desktop

gprege

A package for ranking differentially expressed gene expression time courses…

A package for ranking differentially expressed gene expression time courses through Gaussian process regression. gprege fits two GPs with the an RBF (+ noise diagonal) kernel on each profile. One GP…

SwitchFinder
Dataset

SwitchFinder

Allows for capturing important features of the gene dynamic behaviour.…

Allows for capturing important features of the gene dynamic behaviour. SwitchFinder is a statistical method for the analysis of time-series data, in particular gene expression data, based on a…

Wigwams
Desktop

Wigwams

A computational tool for analysing multiple gene expression time series data…

A computational tool for analysing multiple gene expression time series data sets for the same organism.

EXPANDER
Desktop

EXPANDER EXpression Analyzer and DisplayER

An integrated software platform for the analysis of microarray gene expression…

An integrated software platform for the analysis of microarray gene expression data. EXPANDER is designed to support all the stages of microarray data analysis, from raw data normalization to…

TMRMR
Desktop

TMRMR Temporal Minimum Redundancy-Maximum Relevance

A filter-based feature selection method for temporal gene expression data based…

A filter-based feature selection method for temporal gene expression data based on maximum relevance and minimum redundancy criteria. TMRMR incorporates temporal information by combining relevance,…

NETGEM
Desktop

NETGEM Network Embedded Temporal GEnerative Model

Treats the interaction strengths as random variables which are modulated by…

Treats the interaction strengths as random variables which are modulated by suitable priors. NETGEM is a tractable model rooted in Markov dynamics, for analyzing the dynamics of the interactions…

waveTiling
Desktop

waveTiling

Implements a wavelet-based model for analyzing transcriptome data and extends…

Implements a wavelet-based model for analyzing transcriptome data and extends it towards more complex experimental designs. With waveTiling, the user is able to discover group-wise expressed regions,…

MAPT
Desktop

MAPT Mapping and Analysis of Pathways through Time

Provides an analytical framework to dissect such datasets and ultimately…

Provides an analytical framework to dissect such datasets and ultimately accelerate knowledge discovery through visualization and data-mining. MAPT is a user-friendly tool for both time-series and…

TDARACNE
Desktop

TDARACNE

Detects dependencies between genes at different time delays in order to infer…

Detects dependencies between genes at different time delays in order to infer gene regulatory networks from time-series measurements starting from a well known algorithm based on information theory.…

timecourse
Desktop

timecourse

Offers functions for data analysis and graphical displays for developmental…

Offers functions for data analysis and graphical displays for developmental microarray time course data.

NACEP
Desktop

NACEP Network Based Comparison of Temporal Expression Patterns

Compares temporal gene expression patterns. NACEP compares the temporal…

Compares temporal gene expression patterns. NACEP compares the temporal patterns of a gene between two experimental conditions, taking into consideration all of the possible co-expression modules…

MaTSE
Desktop

MaTSE

It was developed using an iterative software development cycle that involved a…

It was developed using an iterative software development cycle that involved a high level of user feedback and evaluation. MaTSE is an exploratory analysis tool that allows users to find unexpected…

PAICE
Desktop

PAICE Pathway Analysis and Integrated Coloring of Experiments

Utilizes the proven and successful KEGG web-service to map numerical expression…

Utilizes the proven and successful KEGG web-service to map numerical expression onto biochemical pathways. PAICE is a rapid bioinformatics pathway visualization tool for KEGG-compatible accessions…

betr
Desktop

betr Bayesian Estimation of Temporal Regulation

A package to identify differentially expressed genes in microarray time-course…

A package to identify differentially expressed genes in microarray time-course data. BETR explicitly uses the time-dependent structure of the data, employing an empirical Bayes procedure to stabilize…

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