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how_to [2020/02/10 19:46]
admin [Disable scroll acceleration in macOS?]
how_to [2020/05/28 07:33] (current)
shiva [Get familiar with machine learning and its applications in computational biology?]
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 +
 +==== Work with screen sessions? ====
 +
 +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 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+\''​
 +
 +----
 +
  
 ==== 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)? ====
 +
 +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]].
  
 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: 
  
-<​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>​+
  
----- 
- 
-**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? ​==== 
 + 
 +- 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?** \\ + 
-First add the following to your browser (Chrome or Firefox) bookmarks.+==== Get access to the papers through the library when you are off-campus? ​==== 
 + 
 +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.
  
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-**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]].+==== 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]] ​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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-**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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 ==== Access a Bioconductor package source code? ==== ==== Access a Bioconductor package source code? ====
  
-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.,
  
 <​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.
 +
 +----
 +
 +===== 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 [[https://​askubuntu.com/​questions/​356006/​kill-a-screen-session|kill]] your screen: ''​Ctrl+a then Ctrl+\''​
  
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