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how_to [2020/02/04 21:32] – [Install R locally (e.g. on a cluster)?] adminhow_to [2020/02/19 23:16] – [Work with screen session?] shiva
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 ---- ----
 +
 +==== Work with screen session? ====
 +
 +There are five main [[http://www.pixelbeat.org/lkdb/screen.html|commands]] while working with screen session:
 +
 +  - Start and name a screen:
 +
 +<code>
 +screen -S $NAME
 +</code>
 +
 +2. Detach from a screen:
 +
 +<code>
 +Ctrl+a d
 +</code>
 +
 +3. See the list of active screens:
 +
 +<code>
 +screen -ls
 +</code>
 +
 +4. Reattach to a screen:
 +
 +<code>
 +screen -r $NAME
 +</code>
 +
 +5. Quit and kill your screen:
 +
 +<code>
 +Ctrl+a then Ctrl+\
 +</code>
 +
 +----
 +
  
 ==== Read and write excel files in R ==== ==== Read and write excel files in R ====
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-**Get access to the papers through the library when you are off-campus?** \\ +==== Get access to the papers through the library when you are off-campus? ==== 
-First add the following to your browser (Chrome or Firefox) bookmarks.+ 
 +In any of these two ways:\\ 
 +a) First add the following to your browser (Chrome or Firefox) bookmarks.
  
 <code> <code>
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 Then, on the journal page, click on the bookmark. Login and start reading. Then, on the journal page, click on the bookmark. Login and start reading.
 +
 +b) Use [[https://infosec.uthscsa.edu/two-factor-enrollment|GlobalProtect]], which is the University VPN.
  
 ---- ----
  
-**Convert pdf to MS word?** \\+ 
 +==== Convert pdf to MS word? ==== 
 Try whatever you can to avoid conversion! Instead, educate your team and your collaborators to use [[https://www.authorea.com/users/54336|Authorea]], [[https://www.overleaf.com/|Overleaf]] or at least Google Doc. In Google Doc, references can be easily handled using [[https://gsuite.google.com/marketplace/app/paperpile/894076725911|Paperpile]], and figures can be automatically numbered using the the [[https://gsuite.google.com/marketplace/app/cross_reference/269114033347?pann=cwsdp&hl=en|Cross Reference]] add-on as suggested in these [[https://lcolladotor.github.io/2019/04/02/how-to-write-academic-documents-with-googledocs/#.Xjne6RNKjUI|guidelines]] on how to write academic documents with Google Docs . __Only__ if your biologist collaborators cannot [[http://www.dedoimedo.com/computers/latex.html|unfortunately]] edit the LaTeX source, consider using a conversion tool such as docs.[[https://docs.zone/|zone]]. Alternatively, Acrobat Pro can export a .pdf as a .doc file. If Bibtex is not an option, use [[http://www.easybib.com/|EasyBib]]. Try whatever you can to avoid conversion! Instead, educate your team and your collaborators to use [[https://www.authorea.com/users/54336|Authorea]], [[https://www.overleaf.com/|Overleaf]] or at least Google Doc. In Google Doc, references can be easily handled using [[https://gsuite.google.com/marketplace/app/paperpile/894076725911|Paperpile]], and figures can be automatically numbered using the the [[https://gsuite.google.com/marketplace/app/cross_reference/269114033347?pann=cwsdp&hl=en|Cross Reference]] add-on as suggested in these [[https://lcolladotor.github.io/2019/04/02/how-to-write-academic-documents-with-googledocs/#.Xjne6RNKjUI|guidelines]] on how to write academic documents with Google Docs . __Only__ if your biologist collaborators cannot [[http://www.dedoimedo.com/computers/latex.html|unfortunately]] edit the LaTeX source, consider using a conversion tool such as docs.[[https://docs.zone/|zone]]. Alternatively, Acrobat Pro can export a .pdf as a .doc file. If Bibtex is not an option, use [[http://www.easybib.com/|EasyBib]].
  
 ---- ----
  
-**Enable spell check in Emacs on OS X?** \\+ 
 +==== Enable spell check in Emacs on OS X? ==== 
 The default Aquamacs spell checker has some issues. To replace it, first [[http://stackoverflow.com/questions/19022015/emacs-on-mac-os-x-how-to-get-spell-check-to-work|install]] Aspell, which is a [[https://en.wikipedia.org/wiki/GNU_Aspell|replacement]] for Ispell: The default Aquamacs spell checker has some issues. To replace it, first [[http://stackoverflow.com/questions/19022015/emacs-on-mac-os-x-how-to-get-spell-check-to-work|install]] Aspell, which is a [[https://en.wikipedia.org/wiki/GNU_Aspell|replacement]] for Ispell:
  
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-**Do microaray analysis or anything else in Bioconductor?** \\+==== Do microaray analysis or anything else in Bioconductor? ==== 
 [[http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#TOC-Affy|This ]] is an excellent site with many well commented code examples and a lot of handy short-cuts. See also [[:how_to|Functional analysis tools]]. [[http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#TOC-Affy|This ]] is an excellent site with many well commented code examples and a lot of handy short-cuts. See also [[:how_to|Functional analysis tools]].
  
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 ==== Disable scroll acceleration in macOS? ==== ==== 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:+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" of your mouse 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> <code>
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 ---- ----
 +
  
 ===== Choose a solid state (SSD) external drive? ===== ===== Choose a solid state (SSD) external drive? =====