GO2MSIG 20131106 – GO based GSEA Gene Set Generator

GO2MSIG 20131106

:: DESCRIPTION

GO2MSIG generates collections of gene sets in MSigDB format based on the Gene Ontology (GO) project hierarchy and gene association data, for use with the Gene Set Enrichment Analysis (GSEA) implementation available at the Broad Institute. This enables rapid creation of gene set collections for multiple species.

::DEVELOPER

Justin Powell (jacp10 at bioinformatics.org)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • Perl
  • Web Server
  • MySQL

:: DOWNLOAD

 GO2MSIG

:: MORE INFORMATION

SynTReN 1.2 – Generator of Synthetic Gene Expression data for Design and Analysis of Structure Learning algorithms

SynTReN 1.2

:: DESCRIPTION

Syntren  (Synthetic Transcriptional Regulatory Networks) is a network generator that creates synthetic transcriptional regulatory networks and produces simulated gene expression data that approximates experimental data. Network topologies are generated by selecting subnetworks from previously described regulatory networks. Interaction kinetics are modeled by equations based on Michaelis-Menten and Hill kinetics. Our results show that the statistical properties of these topologies more closely approximate those of genuine biological networks than do those of different types of random graph models. Several user-definable parameters adjust the complexity of the resulting data set with respect to the structure learning algorithms.

::DEVELOPER

Kathleen Marchal 

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Java
:: DOWNLOAD

  Syntren

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2006 Jan 26;7:43.
SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms.
Van den Bulcke T, Van Leemput K, Naudts B, van Remortel P, Ma H, Verschoren A, De Moor B, Marchal K.

clinker v0.0.23 – Gene Cluster Comparison Figure Generator

clinker v0.0.23

:: DESCRIPTION

clinker is a pipeline for easily generating publication-quality gene cluster comparison figures.

::DEVELOPER

Chooi Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python

:: DOWNLOAD

clinker

:: MORE INFORMATION

Citation

Gilchrist CLM, Chooi YH.
Clinker & clustermap.js: Automatic generation of gene cluster comparison figures.
Bioinformatics. 2021 Jan 18:btab007. doi: 10.1093/bioinformatics/btab007. Epub ahead of print. PMID: 33459763.

RANDNA – Random DNA Sequence Generator

RANDNA

:: DESCRIPTION

RANDNA is a free software which allows to create random DNA sequences setting both their length and the percentage of nucleotide composition.

::DEVELOPER

Gruppo di Biologia Computazionale

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 RANDNA

:: MORE INFORMATION

Citation:

In Silico Biol. 2006;6(3):253-8.
RANDNA: a random DNA sequence generator.
Piva F1, Principato G.

RENCO 0.3 – A Synthetic Regulatory Network Generator

RENCO 0.3

:: DESCRIPTION

RENCO (REgulatory Network generator with COmbinatorial control) is a C++ based software for automatic generation of ordinary differential equations for gene and protein expression dynamics in artificial regulatory networks.

::DEVELOPER

Roy Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RENCO

:: MORE INFORMATION

Citation

Bioinformatics. 2008 May 15;24(10):1318-20. doi: 10.1093/bioinformatics/btn126. Epub 2008 Apr 8.
A system for generating transcription regulatory networks with combinatorial control of transcription.
Roy S1, Werner-Washburne M, Lane T.

3DRobot 1.0 – Protein Structural Decoy Generator

3DRobot 1.0

:: DESCRIPTION

3DRobot is a program devoted for automated generation of diverse and well-packed protein structure decoys.

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 3DRobot

:: MORE INFORMATION

Citation:

3DRobot: Automated Generation of Diverse and Well-packed Protein Structure Decoys.
Deng H, Jia Y, Zhang Y.
Bioinformatics. 2015 Oct 14. pii: btv601.

GENERATOR 1.02b – Evaluate and Group Incoherently Annotated Genes into Subsets

GENERATOR 1.02b

:: DESCRIPTION

Generator  (GENElist Research Aimed Theme-discovery executOR)  is a tool to evaluate and group incoherently annotated genes into subsets according to their gene ontology (GO) terms.

::DEVELOPER

Petri Pehkonen ( Petri.Pehkonen@uku.fi)

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 Generator

:: MORE INFORMATION

Citation:

Pehkonen P, Wong G and Toronen P. (2005)
Theme discovery from gene lists for identification and viewing of multiple functional groups.
BMC Bioinformatics. 2005; 6: 162.

Exit mobile version