PathVisioRPC – XML-RPC interface for Pathway Analysis tool PathVisio

PathVisioRPC

:: DESCRIPTION

PathVisioRPC is an XML-RPC interface for the pathway analysis tool PathVisio. It allows you to use PathVisio functions to create pathways and visualise and analyse data on pathways in your familiar analytical environment (R, Python, Perl, C++, so on …)

:: SCREENSHOTS

N/A

::DEVELOPER

PathVisioRPC team

::REQUIREMENTS

  • Linux / Solaris / MacOS X
  • Java
  • R

:: DOWNLOAD

 PathVisioRPC

:: MORE INFORMATION

Citation

Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment.
Bohler A, Eijssen LM, van Iersel MP, Leemans C, Willighagen EL, Kutmon M, Jaillard M, Evelo CT.
BMC Bioinformatics. 2015 Aug 23;16:267. doi: 10.1186/s12859-015-0708-8.

LRpath – Pathway Analysis using Logistic Regression

LRpath / RNA-Enrich

:: DESCRIPTION

LRpath performs gene set enrichment testing using logistic regression, and allows the data to remain on a continuous scale. This web-based tool tests against several annotation databases, including Gene Ontology, multiple pathway databases, metabolite, transcription factor and microRNA target sets, and literature-derived annotations. LRpath also includes clustering analysis functionality, allowing you to identify and compare biological concept signatures across multiple studies. LRpath performs well with both small and large sample sizes. Additional benefits of using the LRpath program include (1) the ability to perform both “directional” and “non-directional” enrichment tests that allow for two different perspectives and (2) the ability to easily compare and visualize results across multiple studies using LRpath clustering.

RNA-Enrich is faster than LRpath and best for RNA-seq data that exhibit a relationship between gene read counts and significance of differential gene expression (e.g. genes with higher read counts may have more significant p-values, and vice versa).

::DEVELOPER

The Sartor Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

RNA-Enrich: A cut-off free functional enrichment testing method for RNA-seq with improved detection power.
Lee C, Patil S, Sartor MA.
Bioinformatics. 2015 Nov 25. pii: btv694.

BMC Genomics. 2012 Oct 4;13:526. doi: 10.1186/1471-2164-13-526.
LRpath analysis reveals common pathways dysregulated via DNA methylation across cancer types.
Kim JH1, Karnovsky A, Mahavisno V, Weymouth T, Pande M, Dolinoy DC, Rozek LS, Sartor MA.

Seq2pathway 1.3.0 – Pathway analysis of Next-generation Sequencing data

Seq2pathway 1.3.0

:: DESCRIPTION

Seq2pathway is a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data, consisting of “seq2gene” and “gene2path” components.

::DEVELOPER

Xinan Yang <xyang2 at uchicago.edu>; Bin Wang <binw at uchicago.edu>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • R
  • BioConductor

:: DOWNLOAD

 Seq2pathway

:: MORE INFORMATION

Citation

Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data.
Wang B, Cunningham JM, Yang XH.
Bioinformatics. 2015 May 15. pii: btv289

MetaPath 1.0 – Meta-analysis for Pathway Analysis

MetaPath 1.0

:: DESCRIPTION

MetaPath (Meta-analysis for Pathway Analysis) performs the meta-analysis for pathway enrichment analysis

::DEVELOPER

George C. Tseng 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MetaPath

:: MORE INFORMATION

Citation

Kui Shen and George C. Tseng. (2010)
Meta-analysis for pathway enrichment analysis when combining multiple microarray studies.
Bioinformatics. 26:1316-1323.

directPA 1.2 – Direction Pathway Analysis

directPA 1.2

:: DESCRIPTION

directPA is a package for pathway analysis in experiments with multiple perturbation designs.

::DEVELOPER

Pengyi Yang ,Ellis Patrick

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • R
:: DOWNLOAD

 directPA

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 15;30(6):808-14. doi: 10.1093/bioinformatics/btt616. Epub 2013 Oct 27.
Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway.
Yang P1, Patrick E, Tan SX, Fazakerley DJ, Burchfield J, Gribben C, Prior MJ, James DE, Hwa Yang Y.

PARIS 1.1.3 – Pathway Analysis by Randomization Incorporating Structure

PARIS 1.1.3

:: DESCRIPTION

PARIS is independent of association analysis method and is thus applicable to GWAS datasets of all study designs.

::DEVELOPER

Ritchie Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 PARIS

:: MORE INFORMATION

Citation

Hum Genet. 2011 May;129(5):563-71. doi: 10.1007/s00439-011-0956-2.
Genetic analysis of biological pathway data through genomic randomization.
Yaspan BL, Bush WS, Torstenson ES, Ma D, Pericak-Vance MA, Ritchie MD, Sutcliffe JS, Haines JL.

GO-Elite 1.2.5 – Software for Extended Pathway Analysis

GO-Elite 1.2.5

:: DESCRIPTION

GO-Elite is designed to identify a minimal non-redundant set of biological Ontology terms or pathways to describe a particular set of genes or metabolites.

::DEVELOPER

GO-Elite team

:: SCREENSHOTS

GO-Elite

:: REQUIREMENTS

  • Linux / MacOsX  /Windows

:: DOWNLOAD

 GO-Elite

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Aug 15;28(16):2209-10. doi: 10.1093/bioinformatics/bts366. Epub 2012 Jun 27.
GO-Elite: a flexible solution for pathway and ontology over-representation.
Zambon AC1, Gaj S, Ho I, Hanspers K, Vranizan K, Evelo CT, Conklin BR, Pico AR, Salomonis N.

MetPA – Pathway Analysis and Visualization of Quantitative Metabolomic data

MetPA

:: DESCRIPTION

MetPA (Metabolomics Pathway Analysis) is a free and easy-to-use web application designed to perform pathway analysis and visualization of quantitative metabolomic data

::DEVELOPER

the Wishart Research Group, University of Alberta

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 15;26(18):2342-4. doi: 10.1093/bioinformatics/btq418. Epub 2010 Jul 13.
MetPA: a web-based metabolomics tool for pathway analysis and visualization.
Xia J, Wishart DS.

GEPAT – Genome Expression Pathway Analysis Tool

GEPAT

:: DESCRIPTION

GEPAT (Genome Expression Pathway Analysis Tool) is a modular, scalable and professional-grade software integrating analysis and interpretation of microarray gene expression data.

::DEVELOPER

Department of BioinformaticsBiocenterUniversity of Würzburg, Germany

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

 GEPAT

:: MORE INFORMATION

Citation

Genome Expression Pathway Analysis Tool – Analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context
Markus Weniger , Julia C Engelmann and Jörg Schultz
BMC Bioinformatics 2007, 8:179