ABSTRACT
Ewoud De Troyer, Martin Otava, Jitao David Zhang, Setia Pramana, Tatsiana Khamiakova, Sebastian Kaiser, Martin Sill, Aedin Culhane, Daniel Gusenleitner, Pierre Gestraud, Gabor Csardi, Mengsteab Aregay, Sepp Hochreiter, Gunter Klambauer, Djork-Arne Clevert, Tobias Verbeke, Nolen Joy Perualila, Adetayo Kasim and Ziv Shkedy
20.1 BiclustGUI R package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321 20.1.1 Structure of the BiclustGUI Package . . . . . . . . . . . . . . . . . . . 321 20.1.2 R Commander . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 324 20.1.3 Default Biclustering Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . 325
20.2 Working with the BiclustGUI Package . . . . . . . . . . . . . . . . . . . . . . . . . . 325 20.2.1 Loading the BiclustGUI Package . . . . . . . . . . . . . . . . . . . . . . . 325 20.2.2 Loading the Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 326 20.2.3 Help Documentation and Scripts . . . . . . . . . . . . . . . . . . . . . . . . 326 20.2.4 Export Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 327
20.3 Data Analysis Using the BiclustGUI Package . . . . . . . . . . . . . . . . . . 327 20.3.1 Biclustering with the Plaid Model . . . . . . . . . . . . . . . . . . . . . . 328 20.3.2 Biclustering with ISA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 328 20.3.3 Biclustering with iBBiG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 330 20.3.4 Biclustering with rqubic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 334 20.3.5 Biclustering with BicARE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 336 20.3.6 Robust Biclustering: the s4vd Package . . . . . . . . . . . . . . . . . 339 20.3.7 Biclustering with FABIA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 342
The BiclustGUI R package, a graphical user interface (GUI) developed as a plug-in for R Commander, is an envelope package designed to serve as a platform from which several biclustering algorithms as well as diagnostics tools
Figure 20.1 The structure of the BiclustGUI package.
