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how_to [2020/02/19 13:24] – [Install R locally (e.g. on a cluster)?] admin | how_to [2020/10/06 02:00] – [Work with screen session?] admin |
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| ==== Work with screen sessions? ==== |
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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 of the screen>'' |
| - Detach from a screen: ''Ctrl+a d'' |
| - See the list of active screens: ''screen -ls'' |
| - Reattach to a screen: ''screen -r <NAME of the screen>'' |
| - 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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==== Install R locally (e.g. on a cluster)? ==== | ==== Install R locally (e.g. on a cluster)? ==== |
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| If you want to install the latest __development__ version of R on your macOS, first install [[https://github.com/fxcoudert/gfortran-for-macOS/releases|Fortran]] if you do not have it. You may also need to update [[https://superuser.com/a/664326|PCRE]]. |
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If you do not have sudo permissions, like when you are working on a cluster, you should either use the software module, or install it locally in your home directory. E.g., you can install R on Stampede or Maverick as follows: | If you do not have sudo permissions, like when you are working on a cluster, you should either use the software module, or install it locally in your home directory. E.g., you can install R on Stampede or Maverick as follows: |
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**Write in xls files from R?** \\ | |
Use [[http://www.inside-r.org/packages/cran/XLConnect/docs/writeWorksheetToFile|writeWorksheetToFile]]() function from [[http://cran.r-project.org/web/packages/XLConnect/index.html|XLConnect]] package like below: | |
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<code> | ==== Restore a file deleted in a local git directory? ==== |
writeWorksheetToFile(data=matrix(1:10,2,2),file='./temp.xls',sheet='test1') | |
writeWorksheetToFile(data=matrix(1:6,2,3),file='./temp.xls',sheet='test2') | |
</code> | |
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**Restore a file** **deleted ****in a local git directory?** \\ | |
[[http://stackoverflow.com/questions/9305326/why-doesnt-git-pull-bring-back-directories-that-ive-deleted|Use]] git reset –hard to completely bring your working directory to HEAD state. However, this is a [[http://stackoverflow.com/questions/5473/how-can-i-undo-git-reset-hard-head1|dangerous]] command because you may loose some local files that are not pushed yet. | [[http://stackoverflow.com/questions/9305326/why-doesnt-git-pull-bring-back-directories-that-ive-deleted|Use]] git reset –hard to completely bring your working directory to HEAD state. However, this is a [[http://stackoverflow.com/questions/5473/how-can-i-undo-git-reset-hard-head1|dangerous]] command because you may loose some local files that are not pushed yet. |
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**Get familiar with machine learning and its applications in computational biology? ** \\ | |
| ==== Get familiar with machine learning and its applications in computational biology? ==== |
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| - You can enroll in many online machine learning courses. Some of the best courses in ML can be found [[https://docs.google.com/spreadsheets/d/1AK8lqS-ztMhh8YoOaQ7ScIZmabrQ5AFxAyXKwYWiT04/edit#gid=0|here]]. |
- 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. | - 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. |
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==== Get access to the papers through the library when you are off-campus? ==== | |
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==== ==== | ==== Get access to the papers through the library when you are off-campus? ==== |
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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? ==== | |
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==== ==== | ==== Convert pdf to MS word? ==== |
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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]] add-on, 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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==== Access a Bioconductor package source code? ==== | ==== Access a Bioconductor package source code? ==== |
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It is always better to a install the latest version of a package as directed in the corresponding Bioconductor page (e.g., [[https://bioconductor.org/packages/Pigengene|Pigengene]]). If you need to see more details in the source code, or you need the development version, you can clone the source from the Bioconductor using the "Source Repository (Developer Access) " command, which is posted on the corresponding package [[https://bioconductor.org/packages/release/bioc/html/Pigengene.html|page]], e.g., | It is always better to a install the latest version of a package as directed in the corresponding Bioconductor page (e.g., [[https://bioconductor.org/packages/Pigengene|Pigengene]]). If you need to see more details in the source code, or you need the development version. If the package maintainer adds your public ssh [[https://git.bioconductor.org/BiocCredentials/|key]], then you can clone the source from the Bioconductor using the "Source Repository (Developer Access) " command, which is posted on the corresponding package [[https://bioconductor.org/packages/release/bioc/html/Pigengene.html|page]], e.g., |
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<code> | <code> |
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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? ===== |
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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 [[https://askubuntu.com/questions/356006/kill-a-screen-session|kill]] your screen: ''Ctrl+a then Ctrl+\'' |
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| ===== Search for public domain images? ===== |
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| [[https://unsplash.com/|Unsplash]] is among the best [[https://wcmshelp.ucsc.edu/about-images/finding-public-domain-images.html|resources]] with many hi-resolution images, which are frequently used by media. |
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