Please help to choose Bioconductor R packages and other software for the whole genome sequence data analysis and, in particlular, the goals of false discovery mutation rate, mutations exclusion, mutation contribution and data dimensionality reduction. I could find Expander, MeV, Genesis software for the microarray experiments, however, could not find similar tools for the whole genome sequence analysis of mycobacteria. Sorry, that my question has no code.
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$\begingroup$ What is your question? $\endgroup$– WYSIWYGJan 10, 2015 at 15:04
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1$\begingroup$ This is a good question! why is this getting close votes? it is slightly incoherent and badly written but it definitely merits a response! $\endgroup$– Behzad RowshanravanJan 10, 2015 at 16:06
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$\begingroup$ Have you searched biostars.org? That is a bioinformatics board, and I'd say about half the content is about next gen sequencing. $\endgroup$– swbarnes2Jan 10, 2015 at 17:57
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$\begingroup$ @Bez I voted to close because I think (a) it is broad (b) I am not able to understand what is OP asking for exactly; some kind of all in one package? I retracted the vote but the question needs some clarification. $\endgroup$– WYSIWYGJan 11, 2015 at 6:06
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There are couple of them. First if you want to sequence analysis basic packages are :
http://www.bioconductor.org/help/workflows/high-throughput-sequencing/
Also, Maqweb seems promising.
answered Jan 10, 2015 at 14:07
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$\begingroup$ Add more software, including commercial, please, if you can $\endgroup$ Jan 11, 2015 at 13:46