Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
Next revisionBoth sides next revision
how_to [2019/10/18 20:57] – [Access a Bioconductor package source code?] adminhow_to [2020/01/02 21:21] – [Set local mirror for Rscript] admin
Line 18: Line 18:
 ---- ----
  
-Add only [[http://stackoverflow.com/questions/7124726/git-add-only-modified-changes-and-ignore-untracked-files|modified]] changes and ignore untracked files using git?+=====  Add only  modified  changes and ignore untracked files using git? ===== 
 + 
 +=====   =====
  
 <code> <code>
Line 27: Line 29:
  
 ---- ----
 +
  
 ==== Use a package that is being developed? ==== ==== Use a package that is being developed? ====
Line 193: Line 196:
 ---- ----
  
-**Write a scientific paper?** \\+===== Write a scientific paper? ===== 
 Put the figures together and then [[http://www.scidev.net/global/publishing/practical-guide/how-do-i-write-a-scientific-paper-.html|draft]] different [[https://www.nature.com/articles/nmeth.4532?WT.ec_id=NMETH-201712&spMailingID=55474826&spUserID=MTIyMzczNjc4MDI2S0&spJobID=1285409878&spReportId=MTI4NTQwOTg3OAS2|sections]]. Focus the [[http://www.grantcentral.com/strategies-for-avoiding-common-problems-with-research-manuscripts/|Discussion]]. Be careful about [[http://colah.github.io/posts/2019-05-Collaboration/index.html|authorship]]. Put the figures together and then [[http://www.scidev.net/global/publishing/practical-guide/how-do-i-write-a-scientific-paper-.html|draft]] different [[https://www.nature.com/articles/nmeth.4532?WT.ec_id=NMETH-201712&spMailingID=55474826&spUserID=MTIyMzczNjc4MDI2S0&spJobID=1285409878&spReportId=MTI4NTQwOTg3OAS2|sections]]. Focus the [[http://www.grantcentral.com/strategies-for-avoiding-common-problems-with-research-manuscripts/|Discussion]]. Be careful about [[http://colah.github.io/posts/2019-05-Collaboration/index.html|authorship]].
  
 ---- ----
  
-**Prepare or review computational biology papers for Nature methods?** \\+=====   Prepare or review computational biology papers for Nature methods?   ===== 
 + 
 +=====   ===== 
 Read their "Reviewing computational methods" ([[http://www.nature.com/nmeth/journal/v12/n12/full/nmeth.3686.html|2015]]) and "Guidelines for algorithms and software in Nature Methods" ([[http://blogs.nature.com/methagora/2014/02/guidelines-for-algorithms-and-software-in-nature-methods.html|2014]]) articles. Provide source code, pseudocode, compiled executables, and the mathematical description. Softwares must be accompanied with documentation, sample data and the expected output, and a license (e.g., GPL≥2). Have a look at [[:the_list_of_computational_biology_papers_in_nature_methods|The list of computational biology papers in Nature Methods]] published in 2015, and the [[https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=9&cad=rja&uact=8&ved=0ahUKEwic2Oum3dvJAhUGeSYKHWurD-EQFghQMAg&url=http%3A%2F%2Ford.ntu.edu.tw%2Ftc%2Fincludes%2FGetFile.ashx%3FmID%3D253%26id%3D1744%26chk%3De15262f3-87bf-4a7e-be6a-4103cbc61968&usg=AFQjCNHfNXyryLDQMWBRrInOpJVKIL0LCA&sig2=8C9UE1arY4vi2q_CUdsdiQ|hints]] by an editor of Nature Communications. Read their "Reviewing computational methods" ([[http://www.nature.com/nmeth/journal/v12/n12/full/nmeth.3686.html|2015]]) and "Guidelines for algorithms and software in Nature Methods" ([[http://blogs.nature.com/methagora/2014/02/guidelines-for-algorithms-and-software-in-nature-methods.html|2014]]) articles. Provide source code, pseudocode, compiled executables, and the mathematical description. Softwares must be accompanied with documentation, sample data and the expected output, and a license (e.g., GPL≥2). Have a look at [[:the_list_of_computational_biology_papers_in_nature_methods|The list of computational biology papers in Nature Methods]] published in 2015, and the [[https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=9&cad=rja&uact=8&ved=0ahUKEwic2Oum3dvJAhUGeSYKHWurD-EQFghQMAg&url=http%3A%2F%2Ford.ntu.edu.tw%2Ftc%2Fincludes%2FGetFile.ashx%3FmID%3D253%26id%3D1744%26chk%3De15262f3-87bf-4a7e-be6a-4103cbc61968&usg=AFQjCNHfNXyryLDQMWBRrInOpJVKIL0LCA&sig2=8C9UE1arY4vi2q_CUdsdiQ|hints]] by an editor of Nature Communications.
  
Line 211: Line 218:
  
 ---- ----
 +
  
 ==== Get older versions using git? ==== ==== Get older versions using git? ====
Line 242: Line 250:
 mkdir ~/proj; cd ~/proj mkdir ~/proj; cd ~/proj
 git clone git@git.bioconductor.org:packages/Pigengene git clone git@git.bioconductor.org:packages/Pigengene
 +</code>
 +
 +Now, you can build the package fom the source using:
 +
 +<code>
 +R CMD REMOVE Pigengene; R CMD build Pigengene
 +</code>
 +
 +If the build is successful, a tarbal will be created. You can install the new package using:
 +
 +<code>
 + R CMD INSTALL Pigengene_<Version>.tar.gz
 </code> </code>