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I'm trying to get a handle on what programs different fields of biology use to run statistical tests and other analyses.

  • Ex: R, SPSS, SAS, GraphPad / PRISM, MATLAB, Python, MS Excel, PCORD, STATA, etc.

Please answer with:

  1. Your sub-field of biology
  2. What program you think your field overwhelmingly/generally uses.

    • i.e., what is the "Standard" program for your field?
  3. What program you use

If you share a sub-field / standard with an existing answer, please simply vote/comment. Otherwise add a new answer.

Thanks!

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    $\begingroup$ Note: I understand not all analyses are statistical. I want this post, however, to focus on statistical analyses. Programs used for more nuanced non-statistical analyses can be mentioned in the comments or as additional points in your answer. $\endgroup$ – theforestecologist Jun 6 '17 at 16:02
  • $\begingroup$ I'm just now wondering if this post is inherently biased. I assume (possibly incorrectly) that a large majority of Bio.SE users probably initially joined the SE network for SO (stockOverflow), and so many users here are very likely more programming-software oriented. As such, I wonder if many of our answers (e.g., R and python) are truly accurate for the fields or just popular among biologists with backgrounds with programming-oriented statistics software. [No need to comment; just keep this in mind as you read results]. $\endgroup$ – theforestecologist Dec 1 '17 at 19:03
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Field: Ecology

Standard: R

What I use: R

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    $\begingroup$ As a bioinformatician, my experience is that everyone uses R except wet-lab biologists who use Excel. $\endgroup$ – terdon Jun 6 '17 at 17:15
  • $\begingroup$ @terdon that was my impression, too. But then i started asking around, and some wet-lab folks use Prism. I also know some ecology ppl still using SAS. That got me to wondering how accurate my (and your) assumptions really are... $\endgroup$ – theforestecologist Jun 6 '17 at 17:25
  • $\begingroup$ Well, that was a bit tongue-in-cheek. I'm sure nobody who does statistical analyses regularly uses excel. The people I'm thinking of would just use it for a one-off analysis; they're not stats folks at all. That said, neither am I, of course, which is why I like R: it does the work for me. $\endgroup$ – terdon Jun 6 '17 at 17:26
  • $\begingroup$ @terdon, also if you feel confident about it, please add an answer for bioinformatics. $\endgroup$ – theforestecologist Jun 6 '17 at 17:26
  • $\begingroup$ I'm a wet-lab biologist and I use R! Not really for stats, though. $\endgroup$ – canadianer Jun 6 '17 at 17:54
  • $\begingroup$ @canadianer interesting. What specifically do you use R for? And what do you use for stats? $\endgroup$ – theforestecologist Jun 6 '17 at 19:36
  • $\begingroup$ @theforestecologist Mostly analyzing data from experiments on protein binding kinetics, and preparing figures. I guess in some sense "analyzing data" is statistics, but I'm not doing any statistical tests. $\endgroup$ – canadianer Jun 6 '17 at 21:48
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Field: Bioinformatics (I can speak for genomics, NGS, and systems biology)

Standard: R

What I use: R

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Multiple, so here goes. I assume you don't mind them as a single answer?


Field: Experimental Molecular Biology/Synthetic Biology, & Microbiology

Standard: Excel (sadly). If you can afford it, PRISM.

What I use: R and/or Python


Field: Bioinformatics (Microbial NGS etc.)

Standard: R and/or Python (largely taking over from Perl I think)

What I use: R and Python


Field: Structural Bioinformatics

Standard: Python + C (usually in the form of bespoke software though, e.g. PyMOL)

What I use: Python

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    $\begingroup$ Prism!! Yes!! I love that software. $\endgroup$ – AliceD Aug 6 '17 at 15:13
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    $\begingroup$ Shame more Institutions won't shell out for a license :( $\endgroup$ – Joe Healey Aug 6 '17 at 15:23
  • $\begingroup$ I bought a license for my previous postdoc. My current institution has a license :-) $\endgroup$ – AliceD Aug 6 '17 at 17:33
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Field: Phylogeny

Disclaimer: I'm not active in phylogeny any more (I was until 2013), and I didn't use statistics very often.

Standard: I think that statistical tests part of phylogeny inference procedures tend to be implemented in specific phylogeny reconstruction programs. These are usually written in fast languages (usually C/C++, but I know at least a case using OCaml). I've seen also statistical tests in a Python based package (possibly with C/C++ underlying stuff), and I heard about R packages for phylogeny handling.

What I use(d): Python (scipy.stats)

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Field: Microbial Bioprocesses/White Biotechnologies

Standard: Excel or R

What I use: Excel, R or Python

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Field: Neuroscience

Standard: Matlab

What I use: Matlab

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Field: models of the transmission of infectious disease

Standard: Matlab, R

What I use: Matlab, Fortran.

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