To get some basic information, see our SciVee video about RNAseq, deconvolution of short sequencing reads and abundance prediction for single transcripts or alternative splicing events.
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You can find a steadily growing amount of documentation about the Flux Capacitor and the Flux Simulator in the Flux Wiki. There is also a joint Flux Forum to discuss the current design and future steps.
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The download repository and the issue tracker with bugs and planned improvemens is hosted by Google Code. In order to file new bugs, you have to obtain a free google account.
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