Bioinformatics tools

Basic peak detection – bPeaks (2014)

bPeaks is a R package to identify transcription factor binding sites from ChIPseq data. Our general philosophy is to provide an intuitive tool, well-adapted for small eukaryotic genomes (< 20 Mb). bPeaks uses a combination of 4 cut-offs (T1, T2, T3 and T4) to mimic “good peak” properties as described by biologists who visually inspect the ChIPseq data on a genome browser. For yeast genomes, bPeaks calculates the proportion of peaks that fall in promoter sequences. These peaks are good candidates as transcription factor binding sites. The R package is freely distributed via the CRAN website : http://cran.r-project.org/web/packages/bPeaks. Tutorial and detailed information can also be found here.

ARTIVA (2011)

ARTIVA is a statistical framework to infer time-varying structures of gene-regulation networks. An implementation of the ARTIVA algorithm is available in a R package freely distributed via the CRAN website : http://cran-project.org/web/packages/ARTIVA. Tutorial and detailed information can also be found here.

MitoGenesisDB (2010)

MitoGenesisDB is a database that offers an easy method to mine and visualize information obtained with global mRNA analyses in the yeast S. cerevisiae. MitoGenesisDB couples data mining tools with a user-friendly web interface to obtain a rough snapshot of the transcriptome state during mitochondrial biogenesis. The MitoGenesisDB interface is available at http://www .dsimb.inserm.fr/dsimb_tools/mitgene/.

MiCoViTo (2003)

MiCoViTo is a set of biologists’ tools for exploring, comparing and visualizing changes in the yeast transcriptome by a gene-centric approach. A relational database includes data linked to genome expression and graphical output makes it easy to visualize clusters of co-expressed genes in the context of available biological information. A web interface guides the user during the usage of this tool and is freely accessible at http://www.transcriptome.ens.fr/micovito/.

 

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