Gobbolino – Enumeration of Metabolic Storie

Gobbolino

:: DESCRIPTION

Gobbolino is a software for the enumeration of metabolic stories, which are maximal DAGs with a constrained set of sources and targets.

::DEVELOPER

ERABLE (European Research team in Algorithms and Biology, formaL and Experimental)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Gobbolino

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jan 1;30(1):61-70. doi: 10.1093/bioinformatics/btt597. Epub 2013 Oct 27.
Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure.
Milreu PV1, Klein CC, Cottret L, Acu?a V, Birmelé E, Borassi M, Junot C, Marchetti-Spaccamela A, Marino A, Stougie L, Jourdan F, Crescenzi P, Lacroix V, Sagot MF.

SPRUCE – Somatic Phylogeny Reconstruction using Combinatorial Enumeration

SPRUCE

:: DESCRIPTION

SPRUCE is an algorithm that infers a multi-state perfect phylogeny describing the evolutionary history of the somatic mutations (SNVs and CNVs) of a tumor given multi-sample bulk sequencing data. Specifically, the input to SPRUCE are variant allele frequencies and copy-number mixing proportions for each SNV in each sample.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++

:: DOWNLOAD

SPRUCE

:: MORE INFORMATION

Citation:

El-Kebir M, Satas G, Oesper L, Raphael BJ.
Inferring the Mutational History of a Tumor Using Multi-state Perfect Phylogeny Mixtures.
Cell Syst. 2016 Jul;3(1):43-53. doi: 10.1016/j.cels.2016.07.004. PMID: 27467246.

FACTERA 1.3 – Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm

FACTERA 1.3

:: DESCRIPTION

FACTERA is a tool for practical and robust de novo enumeration of genomic fusions and breakpoints from paired-end targeted (or genome-wide) sequencing data.

::DEVELOPER

Newman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 FACTERA

:: MORE INFORMATION

Citation

FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution.
Newman AM, Bratman SV, Stehr H, Lee LJ, Liu CL, Diehn M, Alizadeh AA.
Bioinformatics. 2014 Aug 20. pii: btu549.

ISMAGS 1.1.3 – Cytoscape app for Motif Enumeration

ISMAGS 1.1.3

:: DESCRIPTION

ISMAGS (InStances of a Motif in A Graph) can numerate all instances of a motif in a graph, making optimal use of the motif’s symmetries.

::DEVELOPER

Van de Peer Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Java
  • Cytoscape

:: DOWNLOAD

ISMAGS

:: MORE INFORMATION

Citation

Bioinformatics. 2017 Feb 1;33(3):461-463. doi: 10.1093/bioinformatics/btw626.
A Cytoscape app for motif enumeration with ISMAGS.
Van Parys T, Melckenbeeck I, Houbraken M, Audenaert P, Colle D, Pickavet M, Demeester P, Van de Peer Y

ICE 1.0.2 – Iterative Clique Enumeration

ICE 1.0.2

:: DESCRIPTION

ICE is an algorithm for the identification of relatively independent cliques as co-expression modules from a gene co-expression network.

::DEVELOPER

the Zhang Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ICE

:: MORE INFORMATION

Citation

BMC Syst Biol. 2010 May 27;4:74. doi: 10.1186/1752-0509-4-74.
Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression.
Shi Z1, Derow CK, Zhang B.

Simcluster 0.9.2 – Clustering Enumeration Gene Expression data on the Simplex Space

Simcluster 0.9.2

:: DESCRIPTION

Simcluster is a package for clustering analysis of transcript enumeration data on the simplex space.

::DEVELOPER

Shmulevich Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Simcluster

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Jul 11;8:246.
Simcluster: clustering enumeration gene expression data on the simplex space.
Vêncio RZ, Varuzza L, de B Pereira CA, Brentani H, Shmulevich I.

OptiCount 201303 – Enumeration of Plankton and Particles

OptiCount 201303

:: DESCRIPTION

OptiCount is a user friendly software for the quantification of phytoplankton, zooplankton and bacterioplankton and even blood cells, particles and other things that cannot be counted automatically.

::DEVELOPER

SequentiX

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

OptiCount

:: MORE INFORMATION

Request a free trial license to use the full spectrum of features for one month and free of charge!