maSigPro 1.56.0 – R package for the analysis of Microarray and RNA-seq Time Series data

maSigPro 1.56.0

:: DESCRIPTION

maSigPro (MicroArray Significant Profiles)is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray experiments.

::DEVELOPER

The Genomics of Gene Expression Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R Package
  • BioConductor

:: DOWNLOAD

 maSigPro

:: MORE INFORMATION

Citation

Next maSigPro: updating maSigPro Bioconductor package for RNA-seq time series.
Nueda MJ, Tarazona S, Conesa A.
Bioinformatics. 2014 Jun 3. pii: btu333.

Bioinformatics. 2006 May 1;22(9):1096-102. Epub 2006 Feb 15.
maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments.
Conesa A1, Nueda MJ, Ferrer A, Talón M.

OLYMPUS – Hybrid Clustering method in Time Series Gene Expression

OLYMPUS

:: DESCRIPTION

OLYMPUS is an automated hybrid clustering method in the field of time series gene expression analysis.

::DEVELOPER

the Biosignal Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 OLYMPUS

:: MORE INFORMATION

Citation

OLYMPUS: an automated hybrid clustering method in time series gene expression. Case study: host response after Influenza A (H1N1) infection.
Dimitrakopoulou K, Vrahatis AG, Wilk E, Tsakalidis AK, Bezerianos A.
Comput Methods Programs Biomed. 2013 Sep;111(3):650-61. doi: 10.1016/j.cmpb.2013.05.025.

DyNB 20150501 – Analyze RNA-seq Time Series data

DyNB 20150501

:: DESCRIPTION

DyNB is novel statistical methodology for analyzing time-course RNA-seq data.

::DEVELOPER

Tarmo Äijö

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab

:: DOWNLOAD

 DyNB

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 15;30(12):i113-20. doi: 10.1093/bioinformatics/btu274.
Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation.
Äijö T, Butty V, Chen Z, Salo V, Tripathi S, Burge CB, Lahesmaa R, Lähdesmäki H.

TimeClust 1.3 – Clustering tool for Gene Expression Time Series

TimeClust 1.3

:: DESCRIPTION

TimeClust is a user-friendly software package to cluster genes according to their temporal expression profiles. It can be conveniently used to analyze data obtained from DNA microarray time-course experiments. It implements two original algorithms specifically designed for clustering short time series together with hierarchical clustering and self-organizing maps.

::DEVELOPER

laboratorio di Bioinformatica e Biologia Sintetica – Univ. of Pavia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 TimeClust

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Feb 1;24(3):430-2. Epub 2007 Dec 6.
TimeClust: a clustering tool for gene expression time series.
Magni P, Ferrazzi F, Sacchi L, Bellazzi R.

LSPR – Detect Periodic Expression Profiles in DNA Microarray Time-series data

LSPR

:: DESCRIPTION

LSPR is a Matlab package used to detect periodic expression profiles in DNA microarray time-series data.

::DEVELOPER

LSPR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • MatLab

:: DOWNLOAD

  LSPR

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Apr 1;27(7):1023-5. doi: 10.1093/bioinformatics/btr041. Epub 2011 Feb 3.
LSPR: an integrated periodicity detection algorithm for unevenly sampled temporal microarray data.
Yang R1, Zhang C, Su Z.

BATS 20080710 – Bayesian Analysis of Time Series Microarray experiments

BATS 20080710

:: DESCRIPTION

BATS is a new user friendly GUI software for Bayesian Analysis of Time Series microarray experiments. It implements a truly functional fully Bayesian approach which allows an user to automatically identify and estimate differentially expressed genes.

::DEVELOPER

Computational & Biology Open laboratory

:: SCREENSHOTS

BATS

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 BATS

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2008 Oct 6;9:415. doi: 10.1186/1471-2105-9-415.
BATS: a Bayesian user-friendly software for analyzing time series microarray experiments.
Angelini C1, Cutillo L, De Canditiis D, Mutarelli M, Pensky M.

Deduce – Deduction of Molecular Reaction Network Structure from Measured Time-series

Deduce

:: DESCRIPTION

Deduce is a now very old but still surprisingly effective correlation-based method of reconstructing molecular reaction networks from time-series data.

::DEVELOPER

The Arkin laboratory 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows/ MacOsX
  • C Compiler

:: DOWNLOAD

 Deduce

:: MORE INFORMATION

BiGGEsTS 1.0.5 – Biclustering Analysis of Time Series Gene Expression Data

BiGGEsTS 1.0.5

:: DESCRIPTION

BiGGEsTS (Biclustering Gene Expression Time Series) is a free and open source software tool providing an integrated environment for the biclustering analysis of time series gene expression data. It offers a complete set of operations for retrieving potentially relevant information from the gene expression data, relying either on visualization or additional techniques for manipulating and processing this particular kind of data.

::DEVELOPER

The Knowledge Discovery and Bioinformatics (KDBIO) groupof INESC-ID

:: SCREENSHOTS

BiGGEsTS

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 BiGGEsTS

:: MORE INFORMATION

Citation

BMC Res Notes. 2009 Jul 7;2:124. doi: 10.1186/1756-0500-2-124.
BiGGEsTS: integrated environment for biclustering analysis of time series gene expression data.
Gonçalve JP, Madeira SC, Oliveira AL.

MetATT – Metabolomics tool for Analyzing Two-factor and Time-series data

MetATT

:: DESCRIPTION

MetATT is a easy-to-use, web-based tool designed for time-series and two-factor metabolomics data analysis. MetATT offers a number of complementary approaches including 3D interactive principal component analysis, two-way heatmap visualization, two-way ANOVA, ANOVA-simultaneous component analysis and multivariate empirical Bayes time-series analysis.

::DEVELOPER

the Wishart Research Group, University of Alberta

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java
  • R package
  • Apache Tomcat 6.0 or Glassfish v2/v3.

:: DOWNLOAD

  MetATT

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Sep 1;27(17):2455-6. doi: 10.1093/bioinformatics/btr392. Epub 2011 Jun 27.
MetATT: a web-based metabolomics tool for analyzing time-series and two-factor datasets.
Xia J, Sinelnikov IV, Wishart DS.

GeneShelf – Web-based Visual Interface for Large Gene Expression Time-series Data Repositories

GeneShelf

:: DESCRIPTION

GeneShelf builds upon a zoomable grid display to represent two categorical dimensions. It also incorporates an augmented timeline with expandable time points that better shows multiple data values for the focused time point by embedding bar charts. We applied GeneShelf to one of the largest microarray datasets generated to study the progression and recovery process of injuries at the spinal cord of mice and rats. There are also considerations of the analysis methods, and the entire data set was converted into three probe set algorithms (Plier, GC-RMA, and dChip), leading to nearly 10,000 microarray data files. SpinalCordLink can provide researchers with a good resource to interactively investigate one of the world largest microarray datasets.

::DEVELOPER

GeneShelf Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 GeneShelf

:: MORE INFORMATION

Citation

IEEE Trans Vis Comput Graph. 2009 Nov-Dec;15(6):905-12.
GeneShelf: a web-based visual interface for large gene expression time-series data repositories.
Kim B, Lee B, Knoblach S, Hoffman E, Seo J.