Tag: Network Analysis

HTSanalyzeR 2.38.0 – Network analysis of High Throughput Screens

HTSanalyzeR 2.38.0

:: DESCRIPTION

HTSanalyzeR provides classes and methods for gene set over-representation, enrichment and network analyses on high-throughput screens.

::DEVELOPER

the Markowetz lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R
  • BioCOnductor

:: DOWNLOAD

 HTSanalyzeR

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Mar 15;27(6):879-80. doi: 10.1093/bioinformatics/btr028. Epub 2011 Jan 22.
HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens.
Wang X1, Terfve C, Rose JC, Markowetz F.

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.

MUFFINN – Cancer Gene Discovery via Network Analysis of Somatic Mutation data

MUFFINN

:: DESCRIPTION

MUFFINN (MUtations For Functional Impact on Network Neighbors) is a method for prioritizing cancer genes accounting for not only for mutations of individual genes but also those of neighbors in functional networks

::DEVELOPER

Network Biomedicine Laboratory at Yonsei University, Korea

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

MUFFINN

:: MORE INFORMATION

Citation

MUFFINN: cancer gene discovery via network analysis of somatic mutation data.
Cho A, Shim JE, Kim E, Supek F, Lehner B, Lee I.
Genome Biol. 2016 Jun 23;17(1):129. doi: 10.1186/s13059-016-0989-x.

atBioNet – Network Analysis Tool for Genomics and Proteomics

atBioNet

:: DESCRIPTION

atBioNet is a free, user friendly, web-based network analysis tool for analyzing, visualizing, and interpreting genomics or proteomics data. The user supplies atBioNet with a list of proteins or genes, and atBioNet then creates an interactive graphical network model that can identify key functional modules. Pathway information from the Kyoto Encyclopedia of Genes and Genomes (KEGG) is directly integrated within atBioNet for enrichment analysis and assessment of the biological meaning of modules.

::DEVELOPER

the National Center for Toxicological Research (NCTR).

:: SCREENSHOTS

 REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 atBioNet

:: MORE INFORMATION

Citation

BMC Genomics. 2012 Jul 20;13(1):325. [Epub ahead of print]
atBioNet – an integrated network analysis tool for genomics and biomarker discovery.
Ding Y, Chen M, Liu Z, Ding D, Ye Y, Zhang M, Kelly R, Guo L, Su Z, Harris SC, Qian F, Ge W, Fang H, Xu X, Tong W.