Mailman 3 January 2020 - fastlmm-user

New releases of FaST-LMM and PySnpTools
by Carl KADIE July 3, 2021

July 3, 2021

I’m happy to announce a new releases of FaST-LMM<https://pypi.org/project/fastlmm/> and PySnpTools<https://pypi.org/project/pysnptools/>. (This release been my “work” since I retired last summer.) The new releases updates both packages to work with the newest version of Pandas, Numpy, and Scikit-learn. The new FaST-LMM release includes single_snp_scale, which allows FaST-LMM to use a cluster and scale to 1 million individuals. See Kadie and Heckerman, bioRxiv 2018<https://www.… [View More]

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FaST-LMM's cluster version now supports multiple phenotypes with almost no extra run time
by Carl KADIE Jan. 29, 2020

Jan. 29, 2020

We've just added support multiple phenotypes. Suppose we wish to analyze 10 phenotypes. We could do 10 separate runs, but that would cost 10 times more in computer resources. (Likewise, 1000 phenotypes would take 1000 times more.) Happily, single_snp_scale can process multiple phenotypes almost as fast as 1. The only extra requirement that is the phenotypes must be prepared so that they have no missing values. See an example in the notebook: https://nbviewer.jupyter.org/github/fastlmm/FaST-… [View More]

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FaST-LMM and PySnpTools now available for Python 3
by Carl KADIE Jan. 11, 2020

Jan. 11, 2020

Dear FaST-LMM/PySnpTools User, I’m happy to report that we’ve just released FaST-LMM for Python 3! Just “pip install fastlmm” or “pip install pysnptools”. See https://pypi.org/project/fastlmm/ for details. Everything from code & notebooks to API examples now runs on both Python 2.7+ and Python 3.7+. Thanks for using FaST-LMM & PySnpTools. Yours, - Carl p.s. If you have ideas on how we can let interested folks know of the new release, please send us an email.

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