From 1631ddcd8d89c20beb77dba29a3bb76bc476f510 Mon Sep 17 00:00:00 2001 From: Elizabeth Hutchins Date: Tue, 18 Dec 2018 12:17:59 -0700 Subject: [PATCH 1/3] fixing/changing/adding links - added link to solutions for R for Data Science - also, the snakemake video link was broken, so added other video link (though maybe there was another tutorial in mind?) - filezilla link was actually cyberduck link; fixed --- README.md | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 9e4472b..5d5ea7d 100644 --- a/README.md +++ b/README.md @@ -73,6 +73,10 @@ Here are videos for how to do basic computation in R, and basic programming in R For advanced R practice, you can run through R for Data Science: http://r4ds.had.co.nz + +R for Data Science solutions are available here: + + https://jrnold.github.io/r4ds-exercise-solutions/ Or you can work in R studio using the swirl R package: @@ -133,14 +137,14 @@ Common SFTP GUIs are CyberDuck: https://cyberduck.io/ And FileZilla: - https://cyberduck.io/ + https://filezilla-project.org/ ## 9. Snakemake One of the first rules of bioinformatics is that it is (nearly) always worth the time to make your analysis reproducible. Snakemake can help you with reproducible analyses. You can start out with this video: - https://youtu.be/naRvlRpXLe8 + https://youtu.be/8xnm_RKkycQ And this tutorial: From 21de79276ebfc0eba87e4ac48a16d0e945ab8023 Mon Sep 17 00:00:00 2001 From: Elizabeth Hutchins Date: Mon, 18 May 2020 16:52:08 -0700 Subject: [PATCH 2/3] overall updates, adding R Shiny and MySQL --- README.md | 25 ++++++++++++++++++++++++- 1 file changed, 24 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 5d5ea7d..da89973 100644 --- a/README.md +++ b/README.md @@ -41,10 +41,13 @@ Alternatively you may want a GUI-based text editor, like Sublime: https://www.sublimetext.com/ +Or Atom: + https://atom.io/ + ## 3. Introduction to python There are many different languages that we can write code or scripts in for analyzing our data. One of the most commonly used langauges in bioinfomatics is python. The tutorial at codecademy can help you get started with learning python syntax, though there are many other places to learn coding in python. - https://www.codecademy.com/learn/python + https://www.codecademy.com/learn/learn-python-3 For advanced python, you can run through the Python Data Science Handbook: @@ -65,6 +68,10 @@ Similar to python, there are many tutorials for R, but one that many trainees in https://www.datacamp.com/courses/free-introduction-to-r +Alternatively, Data Carpentry has in Intro to R course: + + http://datacarpentry.org/R-ecology-lesson/index.html + Here are videos for how to do basic computation in R, and basic programming in R: https://www.youtube.com/watch?v=3xriAzqc-fw @@ -150,3 +157,19 @@ And this tutorial: http://slowkow.com/notes/snakemake-tutorial/ + +## 10. R Shiny +It can be useful to create interactive plots for your data. One way to do this is with R Shiny. + + https://shiny.rstudio.com/tutorial/ + +## 11. Databases - MySQL +Sometimes you may want to create or interact with databases in R. + +Here is an introduction in creating MySQL databases and querying them with R: + + https://programminghistorian.org/en/lessons/getting-started-with-mysql-using-r + +And some information on R Shiny database basics: + + https://shiny.rstudio.com/articles/overview.html From f4b796f5b5fd49ce62f77862f49cfdfcd3bdc449 Mon Sep 17 00:00:00 2001 From: Elizabeth Hutchins Date: Wed, 20 May 2020 11:52:42 -0700 Subject: [PATCH 3/3] add link to maintained repo --- README.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/README.md b/README.md index da89973..0034027 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,7 @@ +This parent repo is no longer maintained. The fork currently being maintained is here: +https://github.com/e-hutchins/BioinformaticsIntroduction + + # Bioinformatics Introduction Here we compile our best practices for introducing new trainees to computational biology.