JBiclustGE

Is an application programming interface (API) developed in the Java language, that comprises 21 biclustering methods to be used in the context of gene expression data analysis. Currently, this application integrates the following biclustering algorithms:

Bayesian Biclustering Model (BBC)
BicFinder
BiMine+
BIclustering by Correlated and Large number of Individual Clustered seeds (BICLIC)
Plaid, Spectral, xMOTIFS, Cheng & Church using the R library biclust as backend.
Bit-Pattern Biclustering Algorithm (BiBit)
FLexible Overlapped biClustering (FLOC) using R library Bicare as backend.
Combinatorial Algorithm for Expression and Sequence-based Cluster Extraction (COALESCE)
Correlated Pattern Biclusters (CPB)
Differentially Expressed BIclusters (DeBi)
Factor Analysis for Bicluster Acquisition (FABIA)
Iterative signature algorithm (ISA)
Order-preserving sub-matrices (OPSM)
BiMax
Penalized Plaid
QUalitative BIClustering (QuBic)
UniBic
UBCLUST

This application also provides additional features such as:

Data preprocessing (Normalization, Standardization, Binarization, Missing values imputation).
Parallel execution of the algorithms (multithread attributes).
Built-in frameworks for the Gene Set Enrichment Analysis (GSEA).
Evaluation measures.
Generation of synthetic datasets.
Visualization of biclustering results (Heatmaps and Parallel coordinates).

Comparison between features provided by JBiclustGE and other relevant biclustering frameworks

Feature	JBiclustGE	BiCAT	biclust	BiBench	MTBA
Programming language	Java	Java	R	Python	Matlab
Number Biclustering algorithms	21	6	6	12	12
Graphical Interface	yes	yes	no	no	no
Requires programming expertise	no	no	yes	yes	yes
Visualization features	yes	yes	yes	yes	yes
Synthetic data	yes	no	no	yes	no
Built-in gene enrichment analysis	yes	no	no	no	no
Post-Processing:
Filtering	yes	yes	no	yes	no
Overlap	yes	yes	yes	yes	yes
Similarity	yes	no	yes	yes	yes
Pairwise analysis	yes	yes	no	yes	no
Coherence	yes	no	yes	no	no
Coverage	yes	no	no	no	no