:: DESCRIPTION
MIxDTrees is a suite of tools for analyzing Gene Expression in the course of development.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Gene expression trees in lymphoid development.
Costa IG, Roepcke S, Schliep A.
BMC Immunol. 2007 Oct 9;8:25.
:: 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
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Peptide identification by database search of mixture tandem mass spectra.
Wang, J., Bourne, P. E., Bandeira, N.
Mol. Cell. Proteomics, 2011
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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)
:: 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
:: 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.
