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…
Desktop app
Short Time-series… Short Time-series Expression Miner

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…

Desktop app
Transcript Time… Transcript Time Course Analysis

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…

SwitchFinder SwitchFinder

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…

Desktop app
EXpression Analyzer… EXpression Analyzer and DisplayER

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…

Desktop app
G T A T C G C T A ImpulseDE ImpulseDE

ImpulseDE

An R package suited to capture single impulse-like progression patterns in high…

An R package suited to capture 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…

Desktop app
Temporal Minimum… Temporal Minimum Redundancy-Maximum Relevance

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,…

Desktop app
MaTSE MaTSE

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…

Desktop app
Wigwams Wigwams

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.

Desktop app
CYCLE CYCLE

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.

Desktop app
gprege gprege

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…

Desktop app
Mfuzz Mfuzz

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).

Desktop app
TDARACNE TDARACNE

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.…

Desktop app
waveTiling waveTiling

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,…

Desktop app
Bayesian Estimation… Bayesian Estimation of Temporal Regulation

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…

Desktop app
maSigPro maSigPro

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…

Desktop app
timecourse timecourse

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.

Advertisements
Join Omic Community

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.