MixDTrees – Mixture of Developmental Trees

MixDTrees

:: DESCRIPTION

MIxDTrees is a suite of tools for analyzing Gene Expression in the course of development.

::DEVELOPER

Ivan Gesteira Costa Filho

:: SCREENSHOTS

MixDTrees

:: REQUIREMENTS

  • Windows
  • MatLab
  • Python

:: DOWNLOAD

 MixDTrees

:: MORE INFORMATION

Citation

Gene expression trees in lymphoid development.
Costa IG, Roepcke S, Schliep A.
BMC Immunol. 2007 Oct 9;8:25.

MixDB 1.0r – Identify Mixture MS/MS Spectra from more than one Peptide

MixDB 1.0r

:: DESCRIPTION

MixDB is a database search tool that able to identify mixture MS/MS spectra from more than one peptide.

::DEVELOPER

CCMS The Center for Computational Mass Spectrometry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows
  • Java
  • Perl

:: DOWNLOAD

   MixDB

:: MORE INFORMATION

Citation:

Peptide identification by database search of mixture tandem mass spectra.
Wang, J., Bourne, P. E., Bandeira, N.
Mol. Cell. Proteomics, 2011

CNT-MD – Coordinate-descent algorithm for the Copy-Number Tree Mixture Deconvolution

CNT-MD

:: DESCRIPTION

CNT-MD is a software for inferring the copy-number profiles of tumor clones and their evolution from fractional copy numbers obtained from multi-sample bulk sequencing data.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

CNT-MD

:: MORE INFORMATION

Citation:

Simone Zaccaria, Mohammed El-Kebir, Gunnar W. Klau, Benjamin J. Raphael:
The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-sample Bulk Sequencing Tumor Data.
RECOMB 2017: 318-335

bgmm 1.8.3 – Belief-based Gaussian Mixture Modeling

bgmm 1.8.3

:: DESCRIPTION

bgmm is an R package for knowledge-based mixture modeling. It implements mixture modeling variants, which differ with respect to the amount of incorporated knowledge, and spread the entire range from unsupervised to supervised modeling.

:: DEVELOPER

Vingron lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 bgmm

:: MORE INFORMATION

Citation

Introducing knowledge into differential expression analysis.
Szczurek E, Biecek P, Tiuryn J, Vingron M.
J Comput Biol. 2010 Aug;17(8):953-67. doi: 10.1089/cmb.2010.0034.

DNC-MIX – Model Distribution of Gene Expression Profile of Test Sample as Mixture of Distributions

DNC-MIX

:: DESCRIPTION

DNC-MIX models the distribution of the gene expression profile of a test sample as a mixture, with each component characterizing the expression levels in a class, and assigns a class label to each test sample

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DNC-MIX

:: MORE INFORMATION

Citation

Alexandridis, R., Lin, S., Irwin, M. (2004)
Class discovery and classification of tumor samples using mixture modeling of gene expression data.
Bioinformatics, 20, 2545-2552.

 

cn.MOPS 1.32.0 – Mixture Of PoissonS for Discovering Copy Number variations in Next Generation Sequencing data

cn.MOPS 1.32.0

:: DESCRIPTION

cn.MOPS is an algorithm that accurately detects copy number variations in next generation sequencing data in a study of multiple samples.

::DEVELOPER

Institute of Bioinformatics, Johannes Kepler University Linz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • R Package
  • BioConductor

:: DOWNLOAD

 cn.MOPS

:: MORE INFORMATION

Citation

Günter Klambauer, Karin Schwarzbauer, Andreas Mayr, Djork-Arné Clevert, Andreas Mitterecker, Ulrich Bodenhofer, Sepp Hochreiter.
cn.MOPS: mixture of Poissons for discovering copy number variations in next generation sequencing data with a low false discovery rate.
Nucleic Acids Research 2012 40(2)

BACOM 1.0 – Bayesian Analysis of COpy number Mixtures

BACOM 1.0

:: DESCRIPTION

BACOM (Bayesian Analysis of COpy number Mixtures) is a statistically-principled in silico approach to accurately estimate genomic deletions and normal tissue contamination, and accordingly recover the true copy number profile in cancer cells. We have developed a cross-platform and open source Java application that implements the whole pipeline of copy number analysis of heterogeneous cancer tissues and other relevant processing steps. We also provide an R interface, bacomR, for running BACOM within the R environment, through which users can smoothly incorporate BACOM into their specific analyses.

::DEVELOPER

Computational Bioinformatics & Bio-imaging Laboratory (CBIL)

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 BACOM

:: MORE INFORMATION

Citation:

BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data.
Yu G, Zhang B, Bova GS, Xu J, Shih IeM, Wang Y.
Bioinformatics. 2011 Jun 1;27(11):1473-80. Epub 2011 Apr 15.