RepExplore – Exploit Technical Replicate Variance in Omics Analysis

RepExplore

:: DESCRIPTION

RepExplore is a web-service dedicated to exploit the information captured in the technical replicate variance to provide more reliable and informative differential expression and abundance statistics for omics datasets.

::DEVELOPER

Bioinformatics Core, Luxembourg Centre for Systems Biomedicine (LCSB)

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

RepExplore: Addressing technical replicate variance in proteomics and metabolomics data analysis.
Glaab E, Schneider R.
Bioinformatics. 2015 Feb 25. pii: btv127

GenePEN – Network Analysis of Omics Data

GenePEN

:: DESCRIPTION

GenePEN, an efficient machine learning approach to identify coordinated alterations of genes or proteins in biological networks using omics data, providing provably optimal results in few seconds

::DEVELOPER

Bioinformatics Core, Luxembourg Centre for Systems Biomedicine (LCSB)

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows/ Linux
  • MatLab

:: DOWNLOAD

 GenePEN

:: MORE INFORMATION

Citation

Stat Appl Genet Mol Biol. 2015 Feb 3. pii: /j/sagmb.ahead-of-print/sagmb-2014-0045/sagmb-2014-0045.xml. doi: 10.1515/sagmb-2014-0045. [Epub ahead of print]
GenePEN: analysis of network activity alterations in complex diseases via the pairwise elastic net.
Vlassis N, Glaab E.

NetGestalt / NetSAM 1.26.0 – Integrating Multidimensional Omics data over Biological Networks

NetGestalt / NetSAM 1.26.0

:: DESCRIPTION

NetGestalt is a data integration framework that allows simultaneous presentation of large-scale experimental and annotation data from various sources in the context of a biological network to facilitate data visualization, analysis, interpretation, and hypothesis generation.

NetSAM (Network Seriation and Modularization) is an R package that takes an edge-list representation of a network as an input and generates files that can be used as an input for the one-dimensional network visualization tool NetGestalt  or other network analysis.

::DEVELOPER

the Zhang Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 NetSAM

:: MORE INFORMATION

Citation

Nat Methods. 2013 Jul;10(7):597-8. doi: 10.1038/nmeth.2517.
NetGestalt: integrating multidimensional omics data over biological networks.
Shi Z, Wang J, Zhang B.

supraHex 1.24.0 – Tabular Omics data analysis using a Supra-hexagonal Map

supraHex 1.24.0

:: DESCRIPTION

supraHex is an open-source R/Bioconductor package for tabular omics data analysis using a supra-hexagonal map

::DEVELOPER

Dr. Hai Fang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 supraHex

:: MORE INFORMATION

Citation:

Biochem Biophys Res Commun. 2014 Jan 3;443(1):285-9. doi: 10.1016/j.bbrc.2013.11.103. Epub 2013 Dec 2.
supraHex: an R/Bioconductor package for tabular omics data analysis using a supra-hexagonal map.
Fang H, Gough J

dnet 1.1.5 – Integrative Analysis of Omics data in terms of Network, Evolution and Ontology

dnet 1.1.5

:: DESCRIPTION

dnet is an open-source R package for omics data integrative analysis in terms of network, evolution and ontology

::DEVELOPER

Dr. Hai Fang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 dnet

:: MORE INFORMATION

Citation:

Genome Med. 2014 Aug 26;6(8):64. doi: 10.1186/s13073-014-0064-8.
The ‘dnet’ approach promotes emerging research on cancer patient survival.
Fang H, Gough J

KeyPathwayMiner 5.0.1 – Combining networks with OMICS data

KeyPathwayMiner 5.0.1

:: DESCRIPTION

KeyPathwayMiner is not limited to analyses of single omics data sets, e.g. gene expression, but is able to directly combine several different omics data types.

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

KeyPathwayMiner

:: REQUIREMENTS

  • Linux / Windows
  • Java
  • Cytoscape

:: DOWNLOAD

 KeyPathwayMiner

:: MORE INFORMATION

Citation

KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape.
Alcaraz N, Pauling J, Batra R, Barbosa E, Junge A, Christensen AG, Azevedo V, Ditzel HJ, Baumbach J.
BMC Syst Biol. 2014 Aug 19;8:99. doi: 10.1186/s12918-014-0099-x.

ChIP-Array 2 – Integrating multiple Omics data to construct Gene Regulatory Networks

ChIP-Array 2

:: DESCRIPTION

ChIP-Array integrates additional types of omics data including long-range chromatin interaction, open chromatin region and histone modification data to dissect more comprehensive GRNs involving diverse regulatory components.

::DEVELOPER

JJWang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web  browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks.
Wang P, Qin J, Qin Y, Zhu Y, Wang LY, Li MJ, Zhang MQ, Wang J.
Nucleic Acids Res. 2015 Apr 27. pii: gkv398.

BioMet Toolbox 2.0 – Genome-wide analysis of Metabolism and Omics data

BioMet Toolbox 2.0

:: DESCRIPTION

The BioMet ToolBox is a web-based resource for exploiting the capabilites of metabolic networks described in genome scale models using flux analysis and random sampling, powered by RAVEN, gene set analysis and basic microarray analysis using PIANO, thereby providing an integrated analysis to identify coregulated subnetwork structures within the metabolic network and also for identifying statistically significant gene sets enabling biological interpretation.

:: DEVELOPER

Systems & Synthetic Biology – SYSBIO, Chalmers University of Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data.
Garcia-Albornoz M, Thankaswamy-Kosalai S, Nilsson A, V?remo L, Nookaew I, Nielsen J.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W175-81. doi: 10.1093/nar/gku371.

mixOmics 5.2.0 – Omics Data Integration Project

mixOmics 5.2.0

:: DESCRIPTION

mixOmics analyses highly dimensional data sets: regularized Canonical Correlation Analysis (‘rCCA’) and sparse Partial Least Squares variants (‘sPLS’) to unravel relationships between two heterogeneous data sets of size (n times p) and (n times q) where the p and q variables are measured on the same samples or individuals n.

::DEVELOPER

mixOmics team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 mixOmics

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Dec 6;13:325. doi: 10.1186/1471-2105-13-325.
A novel approach for biomarker selection and the integration of repeated measures experiments from two assays.
Liquet B1, Lê Cao KA, Hocini H, Thiébaut R.

MT-HESS 0.3 – Simultaneous Association Detection in OMICS Datasets

MT-HESS 0.3

:: DESCRIPTION

MT-HESS is a Bayesain hierarchical model that analyses the association between a large set of predictors, e.g. SNPs (single nucleotide polymorphisms), and many responses, e.g. gene expression, in multiple tissues, cells or conditions.

::DEVELOPER

MT-HESS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/  MacOSX

:: DOWNLOAD

 MT-HESS

:: MORE INFORMATION

Citation

MT-HESS: an efficient Bayesian approach for simultaneous association detection in OMICS datasets, with application to eQTL mapping in multiple tissues.
Lewin A, Saadi H, Peters JE, Moreno-Moral A, Lee JC, Smith KG, Petretto E, Bottolo L, Richardson S.
Bioinformatics. 2015 Oct 26. pii: btv568