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how_to [2019/10/18 20:50] – [Access a Bioconductor package source code?] admin | how_to [2020/01/02 18:21] – [Install Salmon on OSX?] admin |
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**Write a scientific paper?** \\ | ===== Write a scientific paper? ===== |
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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]]. |
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==== Get older versions using git? ==== | ==== Get older versions using git? ==== |
==== 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, 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., |
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<code> | <code> |
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> |
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| Now, you can build the package fom the source using: |
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| <code> |
| R CMD REMOVE Pigengene; R CMD build Pigengene |
| </code> |
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| If the build is successful, a tarbal will be created. You can install the new package using: |
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| <code> |
| R CMD INSTALL Pigengene_<Version>.tar.gz |
</code> | </code> |
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