imDEV 1.4.2 – omics data exploration and visualization in Excel

imDEV 1.4.2

:: DESCRIPTION

imDEV (Interactive modules for Data Exploration and Visualization) is a Microsoft Excel spreadsheet embedded application providing an integrated environment for the analysis of omics data through a user-friendly interface. Individual modules enable interactive and dynamic analyses of large data by interfacing R’s multivariate statistics and highly customizable visualizations with the spreadsheet environment, aiding robust inferences and generating information rich data visualizations. This tool provides access to multiple comparisons with false discovery correction, hierarchical clustering, principal (PCA) and independent component analyses (ICA), partial least squares regression (PLS) and discriminant analysis (PLS-DA), through an intuitive interface for creating high quality two and a three-dimensional visualizations including scatter plot matrices, distribution plots, dendrograms, heat maps, biplots, trellis biplots and  correlation networks.

::DEVELOPER

Dmitry Grapov

:: SCREENSHOTS

imDEV

:: REQUIREMENTS

  •  Excel
  • R package

:: DOWNLOAD

 imDEV

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 1;28(17):2288-90. doi: 10.1093/bioinformatics/bts439. Epub 2012 Jul 18.
imDEV: a graphical user interface to R multivariate analysis tools in Microsoft Excel.
Grapov D, Newman JW.

pwOmics 1.24.0 – Pathway-based data integration of Omics data

pwOmics 1.24.0

:: DESCRIPTION

pwOmics performs pathway-based level-specific data comparison of matching omics data sets based on pre-analysed user-specified lists of differential genes/transcripts and proteins.

::DEVELOPER

Astrid Wachter <Astrid.Wachter at med.uni-goettingen.de>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 pwOmics

:: MORE INFORMATION

Citation

pwOmics: An R package for pathway-based integration of time-series omics data using public database knowledge.
Wachter A, Beissbarth T.
Bioinformatics. 2015 May 21. pii: btv323.

MODMatcher 0.1.0 – Mult-Omics Data Matcher

MODMatcher 0.1.0

:: DESCRIPTION

MODMatcher is a multi-omics data matcher for integrative genomic analysis.

::DEVELOPER

Zhu lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • R

:: DOWNLOAD

 MODMatcher

:: MORE INFORMATION

Citation:

PLoS Comput Biol. 2014 Aug 14;10(8):e1003790. doi: 10.1371/journal.pcbi.1003790. eCollection 2014.
MODMatcher: multi-omics data matcher for integrative genomic analysis.
Yoo S, Huang T, Campbell JD, Lee E1, Tu Z, Geraci MW, Powell CA, Schadt EE, Spira A, Zhu J.

O-miner – Analysis and Annotation of Complex -omics Data

O-miner

:: DESCRIPTION

O-miner is a project designed to automate the analysis and annotation of complex -omics data. The software is easy to use and freely available to the scientific community. Users can upload data via a web page and can be notified by email when their analysis is completed. The output includes detailed data analysis reports and diagrams.

::DEVELOPER

the Barts Cancer Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W560-8. doi: 10.1093/nar/gks432.
O-miner: an integrative platform for automated analysis and mining of -omics data.
Cutts RJ, Dayem Ullah AZ, Sangaralingam A, Gadaleta E, Lemoine NR, Chelala C.

SUMO 1.60i – A Statistical Utility for Microarray and Omics data

SUMO 1.60i

:: DESCRIPTION

SUMO (Statistical Utility for Micro array and Omics data) finds genes / conditions which show statistical differences in their expression between different groups of conditions / genes.

::DEVELOPER

Christian Schwager, Ph. D.

:: SCREENSHOTS

SUMO

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 SUMO

:: MORE INFORMATION

Citation

Radiat Oncol. 2012 May 17;7:70. doi: 10.1186/1748-717X-7-70.
Identification of stable endogenous control genes for transcriptional profiling of photon, proton and carbon-ion irradiated cells.
Sharungbam GD, Schwager C, Chiblak S, Brons S, Hlatky L, Haberer T, Debus J, Abdollahi A.

Paintomics 3 v0.4.5 – Painting Omics Data in Biological Pathways

Paintomics 3 v0.4.5

:: DESCRIPTION

 Paintomics is a web tool for the integration and visualization of transcriptomics and metabolomics data.

::DEVELOPER

The Genomics of Gene Expression Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jan 1;27(1):137-9. Epub 2010 Nov 23.
Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data.
García-Alcalde F, García-López F, Dopazo J, Conesa A.