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how_to [2020/02/18 18:45] – [Install R locally (e.g. on a cluster)?] admin | how_to [2020/02/20 17:40] – [Choose a solid state (SSD) external drive?] admin |
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| ==== Work with screen session? ==== |
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| There are five main [[http://www.pixelbeat.org/lkdb/screen.html|commands]] while working with screen session: |
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| - Start and name a screen: ''screen -S $NAME'' |
| - Detach from a screen: ''Ctrl+a d'' |
| - See the list of active screens: ''screen -ls'' |
| - Reattach to a screen: ''screen -r $NAME'' |
| - Quit and kill your screen: ''Ctrl+a then Ctrl+\'' |
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==== 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. |
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<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. |
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| b) Use [[https://infosec.uthscsa.edu/two-factor-enrollment|GlobalProtect]], which is the University VPN. |
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**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]]. |
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==== Enable spell check in Emacs on OS X? ==== | |
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==== ==== | ==== Enable spell check in Emacs on OS X? ==== |
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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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The non-volatile memory express (NVMe) devices are [[https://ssd.borecraft.com/SSD_Buying_Guide_List.pdf|better]] than SATA solid state drives. Good brands include [[https://smile.amazon.com/gp/product/B07X6CKHH1/ref=ox_sc_act_title_1?smid=A29Y8OP2GPR7PE&psc=1|Sabrent]] (Nano is smaller than Pro but gets hot when extensivly used), Seagete, Addlink, and Team. As of 2020, a speed of 1000 Mb/s is possible using USB 3.2. | The non-volatile memory express (NVMe) devices are [[https://ssd.borecraft.com/SSD_Buying_Guide_List.pdf|better]] than SATA solid state drives. Good brands include [[https://smile.amazon.com/gp/product/B07X6CKHH1/ref=ox_sc_act_title_1?smid=A29Y8OP2GPR7PE&psc=1|Sabrent]] (Nano is smaller than Pro but gets hot when extensivly used), Seagete, Addlink, and Team. As of 2020, a speed of 1000 Mb/s is possible using USB 3.2. |
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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: ''screen -S $NAME'' |
| - Detach from a screen: ''Ctrl+a d'' |
| - See the list of active screens: ''screen -ls'' |
| - Reattach to a screen: ''screen -r $NAME'' |
| - Quit and kill your screen: ''Ctrl+a then Ctrl+\'' |
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