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CLC Main Workbench creates a software environment enabling users to make a large number of advanced DNA, RNA, and protein sequence analyses, combined with gene expression analysis, smooth data management, and excellent graphical viewing and output options.

- Support for both microarray- and sequencing-based (RNA-Seq) expression data
- Visualization: Interactive heat map, table and scatter plot views
- Transformation and normalization tools
- Quality control tools including principal component analysis, MA- and boxplots
- Experimental design tools for two- or multiple group comparisons
- T-tests and ANOVA analysis with support for paired/repeated measures
- Multiple testing corrected p-values (Bonferroni and/or FDR)
- Clustering algorithms: hierarchical clustering, k-means and Partitioning Around Medoids (PAM) with support for various distance and linkage measures.
- Ability to import NetAffx annotation arrays and adding annotation to experiments
- Tools for Gene Set Enrichment Analysis (GSEA) and for Hyper-Geometric based tests for overrepresented annotation categories (e.g. 'GO'stats or specific protein pathways).
- Ability to work with Expression Arrays and RNA-seq results at the same time, enabling comparison of results
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