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how_to [2019/10/11 12:50] – [Use git via proxy or vpn?] adminhow_to [2019/10/20 20:05] – [Access a Bioconductor package source code?] admin
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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, you can clone the source from the Bioconductor mirror, 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, 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>
 mkdir ~/proj; cd ~/proj mkdir ~/proj; cd ~/proj
-git clone https://github.com/Bioconductor-mirror/Pigengene.git+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 createdYou can install the new package using: 
 + 
 +<code> 
 + R CMD INSTALL Pigengene_<Version>.tar.gz
 </code> </code>
  
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 +
  
 ==== Use git via proxy or vpn? ==== ==== Use git via proxy or vpn? ====
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 **Avoid misinterpretation of biological experiments?** \\ **Avoid misinterpretation of biological experiments?** \\
-[[https://www.nature.com/nrc/journal/v17/n7/full/nrc.2017.32.html|Reasoning]] must be logical. Report enough details of the methods to reproduce the results. Assess the robustness of the findings with respect to minor perturbations to the experimental settings. To prove that drug A targets protein X, it is not sufficient to confirm that treatment with A leads to killing cells that have X. Maybe the cells are killed because of some other mechanism. Use "rescue experiments" as in the A=imatinib X=BCR–ABL case.+[[https://www.nature.com/nrc/journal/v17/n7/full/nrc.2017.32.html|Reasoning]] must be logical. Report enough details of the methods to reproduce the results. Assess the robustness of the findings with respect to minor perturbations to the experimental settings. To prove that drug A targets protein X, it is not sufficient to confirm that treatment with A leads to killing cells that have X. Maybe the cells are killed because of some other mechanism. Use "rescue experiments" as in the A=imatinib X=BCR–ABL case. Always, avoid [[https://elifesciences.org/articles/48175|these]] ten common statistical mistakes.
  
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