Voronto – Mapping Gene Expression to Ontologies with Voronoi Tessellations

Voronto

:: DESCRIPTION

Voronto is a tool that integrates expression data and biological ontologies, allowing the analyst to explore the whole ontology and detect changes on expression patterns inside the ontology.

::DEVELOPER

RODRIGO SANTAMARÍA

:: SCREENSHOTS

Voronto

:: REQUIREMENTS

  • Windows / Linux/MacOS
  • Java

:: DOWNLOAD

 Voronto

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 1;28(17):2281-2. doi: 10.1093/bioinformatics/bts428. Epub 2012 Jul 4.
Voronto: mapper for expression data to ontologies.
Santamaría R1, Pierre P.

OncodriveCIS 1.1.0 – Assesses the Influence of Copy Number Alterations (CNA) in the Gene Expression

OncodriveCIS 1.1.0

:: DESCRIPTION

OncodriveCIS  is a method to identify genes that accumulate copy number alterations important for tumour development. This is done by computing the functional impact of CNAs by measuring their effect on the expression of the genes affected.

::DEVELOPER

 The Biomedical Genomics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 OncodriveCIS

:: MORE INFORMATION

Citation

Tamborero D, Lopez-Bigas N and Gonzalez-Perez A.
Oncodrive-CIS: a method to reveal likely driver genes based on the impact of their copy number changes on expression.
PLoS ONE 8(2): e55489. doi:10.1371/journal.pone.0055489

Simulac – Simulator for Complex Gene Expression Circuits

Simulac

:: DESCRIPTION

Simulac is an old but flexible simulator for complex gene expression circuits. Used initially to model complex promoter, elongation, and expression dynamics of the bacteriophage lambda lysis/lysogeny switch.

::DEVELOPER

The Arkin laboratory 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows/ MacOsX
  • C Compiler

:: DOWNLOAD

 Simulac

:: MORE INFORMATION

APPEX 1.0 – Analysis Platform for Identification of Prognostic Gene EXpression Signature in Cancer

APPEX 1.0

:: DESCRIPTION

APPEX is a web-based platform to perform survival analysis, particularly, to support identifying molecular signatures significantly associated with cancer patients’ outcome. APPEX provides various analysis methods to discover genes or any other molecules associated with survival of cancer patients.

::DEVELOPER

Medical Genomics Research Center, KRIBB, Korea.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

APPEX: analysis platform for the identification of prognostic gene expression signatures in cancer.
Kim SK, Kim JH, Yun SJ, Kim WJ, Kim SY.
Bioinformatics. 2014 Aug 4. pii: btu521.

MiningABs 1.0.0 – Mining Associated Biomarkers across multi-connected Gene Expression datasets

MiningABs 1.0.0

:: DESCRIPTION

MiningABs is a new meta-analysis approach  to mine associated biomarkers (ABs) across different array-based datasets.

::DEVELOPER

frazer Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 MiningABs

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2014 Jun 8;15:173. doi: 10.1186/1471-2105-15-173.
MiningABs: mining associated biomarkers across multi-connected gene expression datasets.
Cheng CP, DeBoever C, Frazer KA1, Liu YC, Tseng VS.

pGQL – Analyzing Gene Expression Time Courses

pGQL

:: DESCRIPTION

pGQL (probabilistic Graphical Query Language) is a software tool in particular for analyzing gene expression time courses. It allows its user to interactively define linear HMM queries on time course data using rectangular graphical widgets called probabilistic time boxes. The analysis is fully interactive and the graphical display shows the time courses along with the graphical query. The results can be submitted to gPROF directly from pGQL.

::DEVELOPER

Schliep lab

:: SCREENSHOTS

pGQL

:: REQUIREMENTS

  • Linux/ MacOsX/ Windows
  • Python

:: DOWNLOAD

  pGQL

:: MORE INFORMATION

Citation

BioData Min. 2011 Apr 18;4:9. doi: 10.1186/1756-0381-4-9.
pGQL: A probabilistic graphical query language for gene expression time courses.
Schilling R, Costa IG, Schliep A.

CellMix 1.6.2 – Gene Expression Deconvolution

CellMix 1.6.2

:: DESCRIPTION

CellMix , an R package that incorporates most state-of-the-art deconvolution methods, into an intuitive and extendible framework, providing a single entry point to explore, assess and disentangle gene expression data from heterogeneous samples.

::DEVELOPER

The UCT Computational Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • R package

:: DOWNLOAD

 CellMix

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Sep 1;29(17):2211-2. doi: 10.1093/bioinformatics/btt351. Epub 2013 Jul 3.
CellMix: a comprehensive toolbox for gene expression deconvolution.
Gaujoux R1, Seoighe C.

novoSpaRc 0.4.3 – de novo Spatial Reconstruction of Single-Cell Gene Expression

novoSpaRc 0.4.3

:: DESCRIPTION

novoSpaRc predicts locations of single cells in space by solely using single-cell RNA sequencing data.

::DEVELOPER

N. Rajewsky Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

novoSpaRc

:: MORE INFORMATION

Citation

Moriel N, Senel E, Friedman N, Rajewsky N, Karaiskos N, Nitzan M.
NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport.
Nat Protoc. 2021 Sep;16(9):4177-4200. doi: 10.1038/s41596-021-00573-7. Epub 2021 Aug 4. PMID: 34349282.

ellipsoidFN 0.0.1 – Identifying a Heterogeneous set of Cancer Biomarkers based on Gene Expressions

ellipsoidFN 0.0.1

:: DESCRIPTION

ellipsoidFN (ellipsoid Feature Net) is a software to model the disease complexity by ellipsoids and seek a set of heterogeneous biomarkers.

::DEVELOPER

APORC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux /MacOsX
  • matlab

:: DOWNLOAD

 ellipsoidFN

:: MORE INFORMATION

Citation

Xianwen Ren, Yong Wang, Luonan Chen, Xiang-Sun Zhang, and Qi Jin.
ellipsoidFN: a tool for identifying a heterogeneous set of cancer biomarkers based on gene expressions.
Nucleic Acids Research, 2013 41: e53.

Bicluster – Seed-based Biclustering of Gene Expression Data

Bicluster

:: DESCRIPTION

Bicluster is a seed-based algorithm that identifies coherent genes in an exhaustive, but efficient manner.

::DEVELOPER

AUSTRALIAN PROSTATE CANCER RESEARCH CENTRE.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  •  java

:: DOWNLOAD

 Bicluster

:: MORE INFORMATION

Citation

An J, Liew AW-C, Nelson CC (2012)
Seed-Based Biclustering of Gene Expression Data.
PLoS ONE 7(8): e42431. doi:10.1371/journal.pone.0042431