Peakplot is a Perl implemented freely available software application which labels peptide tandem mass spectra retrospectively after a Mascot database search.
Availability: http://fgcz-peakplot.uzh.ch/
Chipster is a biologist-friendly analysis software for high-throughput data. It contains over 200 analysis tools for next generation sequencing (NGS), microarray and proteomics data. Users can combine tools in automatic analysis workflows, which can be shared. Chipster's interactive visualizations allow users to select datapoints and create new gene lists. For NGS data Chipster contains a built-in genome browser, which highlights SNPs and automatically indexes BAM files and calculates...
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RGnome is a gtk based frontend for GNU R, which is a widely used language for statistical computing. It features a fully working R console and an editor with syntax highlighting.