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how_to [2019/05/31 16:26]
admin [Install R locally (e.g. on a cluster)?]
how_to [2019/09/20 01:38] (current)
admin [Learn about linear models and ANOVA in R?]
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-**Get familiar with applications of machine learning ​in genetics ​and genomics?** \\ +**Get familiar with machine learning and its applications in computational biology? ** \\ 
-First read [[http://​www.nature.com/​nrg/​journal/​v16/​n6/​abs/​nrg3920.html|this]] 2015 review ​paper and then follow its references.+- Most common ML techniques are very well explained in [[https://​scikit-learn.org/​stable/​user_guide.html|Scikit learn]] with [[https://​scikit-learn.org/​stable/​modules/​decomposition.html|illustrations]] and example Python code. These techniques have been implemented in [[https://​www.kaggle.com/​getting-started/​5243|R]] packages including mlr3 and tidymodels. 
 + 
 +-[[http://​www.nature.com/​nrg/​journal/​v16/​n6/​abs/​nrg3920.html|This]] 2015 paper reviews applications of ML in genetics and genomics. Read it and follow its references.
  
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 <​code>​ <​code>​
-brew install aspell ​--with-lang-en+brew install aspell
 </​code>​ </​code>​
  
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-**Begin learning bioinformatics?​** \\+ 
 +====   Begin learning bioinformatics? ​  ==== 
 Take a course from the [[http://​research.omicsgroup.org/​index.php/​List_of_free_online_bioinformatics_courses|list]] of free online bioinformatics courses e.g., the Computational Molecular Biology [[http://​cmgm.stanford.edu/​biochem218/​index.html|Course]] at Stanford is broad and covers the classic topics but it is not updated, and may become outdated. The same is true for PLOS Translational Bioinformatics [[http://​collections.plos.org/​translational-bioinformatics|Collection]] of articles, which are more advanced. Most central topics are covered in some course from the European Bioinformatics Institute ([[https://​www.ebi.ac.uk/​training/​online/​course-list|EBI]]). Very useful training materials are available from [[https://​www.mygoblet.org/​|GOBLET]]. Videos from the Models, Inference & Algorithms Initiative ([[https://​www.broadinstitute.org/​scientific-community/​science/​mia/​models-inference-algorithms|MIA]]) at Broad are relatively advanced.\\ Take a course from the [[http://​research.omicsgroup.org/​index.php/​List_of_free_online_bioinformatics_courses|list]] of free online bioinformatics courses e.g., the Computational Molecular Biology [[http://​cmgm.stanford.edu/​biochem218/​index.html|Course]] at Stanford is broad and covers the classic topics but it is not updated, and may become outdated. The same is true for PLOS Translational Bioinformatics [[http://​collections.plos.org/​translational-bioinformatics|Collection]] of articles, which are more advanced. Most central topics are covered in some course from the European Bioinformatics Institute ([[https://​www.ebi.ac.uk/​training/​online/​course-list|EBI]]). Very useful training materials are available from [[https://​www.mygoblet.org/​|GOBLET]]. Videos from the Models, Inference & Algorithms Initiative ([[https://​www.broadinstitute.org/​scientific-community/​science/​mia/​models-inference-algorithms|MIA]]) at Broad are relatively advanced.\\
 \\ \\
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-**Install Salmon on OSX?** \\+==== Install Salmon on OSX? ==== 
 + 
 +\\
 If you do not have autoconf, [[http://​mac-dev-env.patrickbougie.com/​autoconf/​|install]] it. Following the installation guidelines, for OSX you need to first [[http://​stackoverflow.com/​questions/​3181468/​how-do-you-install-intel-tbb-on-os-x|install]] Thread Building Blocks (TBB) (brew install tbb) and then check that the installation was successful (brew list). Download the latest [[https://​github.com/​COMBINE-lab/​salmon/​releases|version]] of Salmon source code and uncompress it. Follow Salmon'​s installation [[http://​salmon.readthedocs.org/​en/​latest/​building.html#​installation|guidelines]]. The cmake command in the guidelines will be something like the following for OSX: If you do not have autoconf, [[http://​mac-dev-env.patrickbougie.com/​autoconf/​|install]] it. Following the installation guidelines, for OSX you need to first [[http://​stackoverflow.com/​questions/​3181468/​how-do-you-install-intel-tbb-on-os-x|install]] Thread Building Blocks (TBB) (brew install tbb) and then check that the installation was successful (brew list). Download the latest [[https://​github.com/​COMBINE-lab/​salmon/​releases|version]] of Salmon source code and uncompress it. Follow Salmon'​s installation [[http://​salmon.readthedocs.org/​en/​latest/​building.html#​installation|guidelines]]. The cmake command in the guidelines will be something like the following for OSX:
  
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 **Set the default width of fill mode (line length) in emacs?** \\ **Set the default width of fill mode (line length) in emacs?** \\
-[[http://​stackoverflow.com/​questions/​3566727/​how-to-set-the-default-width-of-fill-mode-to-80-with-emacs|Use]] 'M-x customize-variable'​ to set '​fill-column'​ (100 in Oncinfo). Use DejaVu Sans Mono (~[[http://​www.leancrew.com/​all-this/​2009/​10/​the-compleat-menlovera-sans-comparison/​|Menlo]] on MacOS) size 18-20 is an [[http://​ergoemacs.org/​emacs/​emacs_unicode_fonts.html|appropriate]] font for programming in Emacs. To do so, you may need to manually edit your .emacs in [[https://​stackoverflow.com/​questions/​4821984/​emacs-osx-default-font-setting-does-not-persist|macOS]].+[[http://​stackoverflow.com/​questions/​3566727/​how-to-set-the-default-width-of-fill-mode-to-80-with-emacs|Use]] 'M-x customize-variable'​ to set '​fill-column'​ (100 in Oncinfo). Use DejaVu Sans Mono (~[[http://​www.leancrew.com/​all-this/​2009/​10/​the-compleat-menlovera-sans-comparison/​|Menlo]] on MacOS) size 18-20 is an [[http://​ergoemacs.org/​emacs/​emacs_unicode_fonts.html|appropriate]] font for programming in Emacs. To do so, you may need to manually edit your .emacs in [[https://​stackoverflow.com/​questions/​4821984/​emacs-osx-default-font-setting-does-not-persist|macOS]], and add the following [[https://​stackoverflow.com/​questions/​4879785/​can-i-break-the-long-line-in-emacs-non-windows-to-the-next-line|line]]:​ 
 + 
 +<​code>​ 
 +(setq truncate-lines nil) 
 +</​code>​
  
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-**Get older versions using git?** \\+==== Get older versions using git? ==== 
 [[https://​githowto.com/​getting_old_versions|Use]] "git log" to see the previous commits and the corresponding hashes, "git checkout <​hash>"​ to get an older version, and "git checkout master"​ to get back. [[https://​githowto.com/​getting_old_versions|Use]] "git log" to see the previous commits and the corresponding hashes, "git checkout <​hash>"​ to get an older version, and "git checkout master"​ to get back.
  
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-**Learn about linear models and ANOVA in R?** \\+ 
 +==== Learn about linear models and ANOVA in R? ==== 
 Review Advanced Statistical Methods II lecture [[https://​www.utdallas.edu/​~ammann/​stat6338/​stat6338.html|notes]] by Dr. Larry Ammann at UT Dallas. Review Advanced Statistical Methods II lecture [[https://​www.utdallas.edu/​~ammann/​stat6338/​stat6338.html|notes]] by Dr. Larry Ammann at UT Dallas.
  
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 ==== Aks people'​s opinion? ==== ==== Aks people'​s opinion? ====
  
-Create a [[https://​doodle.com/​|Doodle]] to find a common time for scheduling events. For longer surveys, use [[https://​www.surveymonkey.com/​|SurveyMonkey]] for offline, and [[https://​www.pollev.com/​|Poll]] Everywhere for online interaction with audiance.+Create a [[https://​doodle.com/​|Doodle]] to find a common time for scheduling events. For longer surveys, use [[https://​www.surveymonkey.com/​|SurveyMonkey]] for offline, and [[https://​www.pollev.com/​|Poll]] Everywhere for online interaction with audience. 
 + 
 +---- 
 + 
 +==== Disable scroll acceleration in macOS? ==== 
 + 
 +Install and [[https://​www.reddit.com/​r/​osx/​comments/​6kx6zb/​how_to_disable_mouse_scrolling_acceleration/​|use]] USB [[http://​www.usboverdrive.com/​USBOverdrive/​Information.html|Overdrive]] to set Wheel up and down "​Speed"​ to say, 6 lines. The following [[https://​apple.stackexchange.com/​questions/​253111/​how-to-disable-scroll-acceleration-in-macos-sierra|command]] does NOT work: 
 + 
 +<​code>​ 
 +defaults write .GlobalPreferences com.apple.scrollwheel.scaling -1 
 +</​code>​ 
 + 
 +Logitech Control Center may help on the [[https://​support.logi.com/​hc/​en-gb/​articles/​360025297833-Logitech-Control-Center-for-Macintosh-OS-X|Logitech]] MX mice older than 2019.