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.

GMFilter 1.0.0 – Improves GeneMapper Analysis by removing bad wells

GMFilter 1.0.0

:: DESCRIPTION

GMFilter is a Windows program for improving GeneMapper® analysis of 384 well SNPlex™ plates by removing bad wells, i.e. wells having a low signal intensity across all assays. This is done by creating a normal MS-DOS batch file, which deletes .fsa files of wells having a median signal intensity below a specified quality threshold. Afterwards the GeneMapper® analysis can be repeated with a standard analysis method (we recommend “RelaxedRules”, see below).

::DEVELOPER

Institute for Clinical Molecular Biology

:: SCREENSHOTS

::REQUIREMENTS

  • Windows

:: DOWNLOAD

 GMFilter

:: MORE INFORMATION

Citation

Teuber M, Wenz MH, Schreiber S, Franke A (2009).
GMFilter and SXTestPlate: software tools for improving the SNPlex(TM) genotyping system.
BMC Bioinformatics 10(1):81

Genomizer 1.2.0 – Analysis of Genome Wide Association Experiments

Genomizer 1.2.0

:: DESCRIPTION

Genomizer is a platform independent Java program for the analysis of genome wide association experiments.The software implements the workflow of an association experiment, including data management, single-point and haplotype analysis, “lead” definition, and data visualization.

::DEVELOPER

Institute for Clinical Molecular Biology

:: SCREENSHOTS

::REQUIREMENTS

:: DOWNLOAD

 Genomizer

:: MORE INFORMATION

Citation

Franke A, Wollstein A, Teuber M, Wittig M, Lu T, Hoffmann K, Nurnberg P, Krawczak M, Schreiber S, Hampe J (2006).
GENOMIZER: an integrated analysis system for genome-wide association data.
Human Mutat 27(6):583-588

ErmineJ 3.2 – Analysis of Gene sets in Expression Microarray data

ErmineJ 3.2

:: DESCRIPTION

ErmineJ performs analyses of gene sets in expression microarray data. A typical goal is to determine whether particular biological pathways are “doing something interesting” in the data. The software is designed to be used by biologists with little or no informatics background.

::DEVELOPER

Pavlidis lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • java

:: DOWNLOAD

 ErmineJ

:: MORE INFORMATION

Citation

Lee H.K., Braynen W., Keshav K. and Pavlidis P. (2005)
ErmineJ: Tool for functional analysis of gene expression data sets.
BMC Bioinformatics 6:269.

AVAtar 0.4.11 – Analysis and Visualization of Alteration data

AVAtar 0.4.11

:: DESCRIPTION

Avatar features interactively customizable alteration plots, extensive data import capabilities and a multi-objective optimization algorithm to find alteration patterns, e.g. gene sets with mutually exclusive alterations or small gene sets with high sample coverage.

::DEVELOPER

Medical Systems Biology, University of Ulm

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Java

:: DOWNLOAD

AVAtar

:: MORE INFORMATION

Citation

Völkel G, Laban S, Fürstberger A, Kühlwein SD, Ikonomi N, Hoffman TK, Brunner C, Neuberg DS, Gaidzik V, Döhner H, Kraus JM, Kestler HA.
Analysis, identification and visualization of subgroups in genomics.
Brief Bioinform. 2021 May 20;22(3):bbaa217. doi: 10.1093/bib/bbaa217. Erratum in: Brief Bioinform. 2021 Jul 06;: PMID: 32954413; PMCID: PMC8138884.

Ebbie 3.0.9 – Analysis & Storage of Small RNA Cloning Data

Ebbie 3.0.9

:: DESCRIPTION

Ebbie is a semi-automated smRNA cloning data processing algorithm, which initially searches for any substring within a DNA sequencing text file, which is flanked by two constant strings. The substring, also termed smRNA or insert, is stored in a MySQL and BlastN database. These inserts are then compared using BlastN to locally installed databases allowing the rapid comparison of the insert to both the growing smRNA database and to other static sequence databases.

::DEVELOPER

H Alexander Ebhardt

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Ebbie

:: MORE INFORMATION

Citation

H Alexander Ebhardt , Kay C Wiese and Peter J Unrau
Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server
BMC Bioinformatics 2006, 7:185doi:10.1186/1471-2105-7-185

ESPRIT-Tree 1.2 – Hierarchical Clustering Analysis of Massive Sequence data

ESPRIT-Tree 1.2

:: DESCRIPTION

ESPRIT-Tree is a software for hierarchical clustering analysis of massive sequence data.

::DEVELOPER

Bioinformatics Laboratory, SUNY Buffalo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  ESPRIT-Tree

:: MORE INFORMATION

Citation:

Y. Cai and Y. Sun
ESPRIT-Tree: Hierarchical Clustering Analysis of Millions of 16S rRNA Pyrosequences in Quasilinear Time,
Nucleic Acids Research, vol. 39, no. 14, e95, 2011. (impact factor: 7.8)

Spines 1.15 – C++ Software Package for Genomic Sequence Alignment and Analysis

Spines 1.15

:: DESCRIPTION

Spinesis a C++ software package for genomic sequence alignment and analysis.

::DEVELOPER

The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

   Spines

:: MORE INFORMATION

Citation

Grabherr MG, Russell P, Meyer M, Mauceli E, Alfoldi J, Di Palma F, Lindblad-Toh K.
Genome-wide synteny through highly sensitive sequence alignment: Satsuma.
Bioinformatics. 2010 May 1;26(9):1145-51. Epub 2010 Mar 5

ReadXplorer 2.2.3 – Visualization and Analysis of Mapped Sequences

ReadXplorer 2.2.3

:: DESCRIPTION

ReadXplorer is a freely available comprehensive exploration and evaluation tool for NGS data. It extracts and adds quantity and quality measures to each alignment in order to classify the mapped reads. This classification is then taken into account for the different data views and all supported automatic analysis functions.

::DEVELOPER

Bioinformatics and Systems Biology, Justus-Liebig-University

:: SCREENSHOTS

ReadXplorer

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 ReadXplorer

:: MORE INFORMATION

Citation

Hilker R, Stadermann KB, Schwengers O, Anisiforov E, Jaenicke S, Weisshaar B, Zimmermann T, Goesmann A.
ReadXplorer 2-detailed read mapping analysis and visualization from one single source.
Bioinformatics. 2016 Dec 15;32(24):3702-3708. doi: 10.1093/bioinformatics/btw541. Epub 2016 Aug 18. PMID: 27540267; PMCID: PMC5167064.

Bioinformatics. 2014 Apr 30. [Epub ahead of print]
ReadXplorer – Visualization and Analysis of Mapped Sequences.
Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A.

inGAP 3.1.1 – Integrated Next-gen Genome Analysis Platform

inGAP 3.1.1

:: DESCRIPTION

inGAP is an integrated platform for next-generation sequencing project, the core function of which is to detect SNPs and indels using a Bayesian algorithm.It does not have any read length restriction. It can handle 454 sequencing and/or Illumina Solexa sequencing and/or Sanger sequencing data sets.

::DEVELOPER

Ji Qi (qij@fudan.edu.cn) and Fangqing Zhao (zhfq@mail.biols.ac.cn)

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX

:: DOWNLOAD

 inGAP

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Jan 1;26(1):127-9. Epub 2009 Oct 30.
inGAP: an integrated next-generation genome analysis pipeline.
Qi J, Zhao F, Buboltz A, Schuster SC.
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