Has anyone used bioconductor from Python? Is there any reason I would choose to use it from R instead of Python? It seems like there is a Python extension for it. Also, is there any reason to use bioconductor over Biopython?

  • $\begingroup$ My understanding is no, but for a Bioconductor specialist how knows Python they'll be aware of comparable packages mainly via Biopython $\endgroup$ – M__ May 10 '20 at 14:51
  • $\begingroup$ don't quite get your question.. is there something you need to use one or the other for? The link you have uses rpy2, basically calling R from inside python.. not so easy for you to pass objects from rpy2 back into python $\endgroup$ – StupidWolf May 10 '20 at 17:49
  • $\begingroup$ My experience of rpy2 using ggplot2 was that it sucked hard and it was better to use Matplotlib and seabourne, i.e. the inbuilt graphing programs of Python, albeit less powerful than ggplot2 $\endgroup$ – M__ May 10 '20 at 18:05

Bioconductor packages are R packages that can only be used directly from python via rpy2 or similar. If you've ever had reason to use rpy2 you'd probably realize quickly that while it works, it's no where near as easy as doing the same thing directly in R.

Biopython is a package for doing a number of useful things, but it can in no way come remotely close to performing even a percent of what Bioconductor packages do. That would be an impossible feat for a single python package.

  • $\begingroup$ Thanks for replying. So is there a way to work around not using R (and use Python instead) while still being able to do what Bioconductor can do? Is there an ecosystem of Python packages along with Biopython that can emulate what can be done with Bioconductor to a certain extent? $\endgroup$ – An Ignorant Wanderer May 10 '20 at 20:13
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    $\begingroup$ There is no python equivalent to Bioconductor. If you need to perform a statistical analysis you need to learn R. $\endgroup$ – Devon Ryan May 10 '20 at 20:15

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