- Curse: Building expression atlases and co-expression networks from public RNA-Seq data. Vaneechoutte and Vandepoele,
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- PLAZA, a resource for plant comparative genomics. Proost et al., 2009 - Van Bel et al., 2012 - Proost et al., 2015
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- pico-PLAZA, a resource for algal comparative genomics. Vandepoele et al., 2013
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- TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information. Kulkarni et al.,
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- TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes. Van Bel et al., 2013
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- ATCOECIS, a toolbox to study transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks. Vandepoele et al., 2009
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- SPPG, Sequence Platform for the phylogenetic analysis of Plant Genes. Vandepoele et al., 2005
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