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how_to [2019/09/19 22:37] – [Get older versions using git?] admin | how_to [2019/10/11 12:53] – [Use git via proxy or vpn?] admin |
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==== Get older versions using git? ==== | ==== Get older versions using git? ==== |
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[[https://githowto.com/getting_old_versions|Use]] "git log" to see the previous commits and the corresponding hashes, "git checkout <hash>" to get an older version, and "git checkout master" to get back. | [[https://githowto.com/getting_old_versions|Use]] "git log" to see the previous commits and the corresponding hashes, "git checkout <hash>" to get an older version, and "git checkout master" to get back. |
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==== Learn about linear models and ANOVA in R? ==== | |
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\\ | ==== Learn about linear models and ANOVA in R? ==== |
Review Advanced Statistical Methods II lecture [[https://www.utdallas.edu/~ammann/stat6338/stat6338.html|notes]] by Dr. Larry Ammann at UT Dallas. | Review Advanced Statistical Methods II lecture [[https://www.utdallas.edu/~ammann/stat6338/stat6338.html|notes]] by Dr. Larry Ammann at UT Dallas. |
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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, you can clone the source from the Bioconductor mirror, e.g., |
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**Use git via proxy or vpn?** \\ | ==== Use git via proxy or vpn? ==== |
Use [[https://github.com/apenwarr/sshuttle|sshuttle]], e.g., sshuttle -r h_[[mailto:z14@nyx.cs.txstate.edu|mailto:z14@nyx.cs.txstate.edu]] 0.0.0.0/0 -vv\\ | Use [[https://github.com/apenwarr/sshuttle|sshuttle]], e.g., sshuttle -r h_[[mailto:z14@nyx.cs.txstate.edu|mailto:z14@nyx.cs.txstate.edu]] 0.0.0.0/0 -vv\\ |
The list of servers at Texas Sate University are listed [[https://cs.txstate.edu/resources/labs/accounts/linux/|here]]. | The list of servers at Texas Sate University are listed [[https://cs.txstate.edu/resources/labs/accounts/linux/|here]]. |
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**Silence a gene?** \\ | **Silence a gene?** \\ |
Small interfering (si) RNAs and miRNAs [[https://www.youtube.com/watch?v=cK-OGB1_ELE|bindd ]] to mRAN and prevent it from being translated. | Small interfering (si) RNAs and miRNAs [[https://www.youtube.com/watch?v=cK-OGB1_ELE|bind ]]to mRAN and prevent it from being translated. |
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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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