Literature DB >> 15145813

ClutrFree: cluster tree visualization and interpretation.

Ghislain Bidaut1, Michael F Ochs.   

Abstract

UNLABELLED: ClutrFree facilitates the visualization and interpretation of clusters or patterns computed from microarray data through a graphical user interface that displays patterns, membership information of the genes and annotation statistics simultaneously. ClutrFree creates a tree linking the patterns based on similarity, permitting the navigation among patterns identified by different algorithms or by the same algorithm with different parameters, and aids the inferring of conclusions from a microarray experiment. AVAILABILITY: The ClutrFree Java source code and compiled bytecode are available as a package under the GNU General Public License at http://bioinformatics.fccc.edu

Mesh:

Year:  2004        PMID: 15145813     DOI: 10.1093/bioinformatics/bth307

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  11 in total

1.  Matrix Factorization for Transcriptional Regulatory Network Inference.

Authors:  Michael F Ochs; Elana J Fertig
Journal:  IEEE Symp Comput Intell Bioinforma Comput Biol Proc       Date:  2012-05

2.  Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species.

Authors:  Genevieve L Stein-O'Brien; Brian S Clark; Thomas Sherman; Cristina Zibetti; Qiwen Hu; Rachel Sealfon; Sheng Liu; Jiang Qian; Carlo Colantuoni; Seth Blackshaw; Loyal A Goff; Elana J Fertig
Journal:  Cell Syst       Date:  2019-05-22       Impact factor: 10.304

Review 3.  Matrix factorisation methods applied in microarray data analysis.

Authors:  Andrew V Kossenkov; Michael F Ochs
Journal:  Int J Data Min Bioinform       Date:  2010       Impact factor: 0.667

4.  Matrix factorization for recovery of biological processes from microarray data.

Authors:  Andrew V Kossenkov; Michael F Ochs
Journal:  Methods Enzymol       Date:  2009       Impact factor: 1.600

5.  Matrix factorization and transfer learning uncover regulatory biology across multiple single-cell ATAC-seq data sets.

Authors:  Rossin Erbe; Michael D Kessler; Alexander V Favorov; Hariharan Easwaran; Daria A Gaykalova; Elana J Fertig
Journal:  Nucleic Acids Res       Date:  2020-07-09       Impact factor: 16.971

6.  A Mechanism of Resistance to Antibody-Targeted Immune Attack.

Authors:  Dalal S Aldeghaither; David J Zahavi; Joseph C Murray; Elana J Fertig; Garrett T Graham; Yong-Wei Zhang; Allison O'Connell; Junfeng Ma; Sandra A Jablonski; Louis M Weiner
Journal:  Cancer Immunol Res       Date:  2018-12-18       Impact factor: 12.020

7.  LS-NMF: a modified non-negative matrix factorization algorithm utilizing uncertainty estimates.

Authors:  Guoli Wang; Andrew V Kossenkov; Michael F Ochs
Journal:  BMC Bioinformatics       Date:  2006-03-28       Impact factor: 3.169

8.  BayGO: Bayesian analysis of ontology term enrichment in microarray data.

Authors:  Ricardo Z N Vêncio; Tie Koide; Suely L Gomes; Carlos A de B Pereira
Journal:  BMC Bioinformatics       Date:  2006-02-23       Impact factor: 3.169

9.  Determination of strongly overlapping signaling activity from microarray data.

Authors:  Ghislain Bidaut; Karsten Suhre; Jean-Michel Claverie; Michael F Ochs
Journal:  BMC Bioinformatics       Date:  2006-02-28       Impact factor: 3.169

10.  MADIBA: a web server toolkit for biological interpretation of Plasmodium and plant gene clusters.

Authors:  Philip J Law; Clotilde Claudel-Renard; Fourie Joubert; Abraham I Louw; Dave K Berger
Journal:  BMC Genomics       Date:  2008-02-28       Impact factor: 3.969

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