Tutorial to learn Data Science in R from Scratch

Here’s a list of useful bookmarks when learning to code with data or coding for research. You can either check out links individually or if you want the whole list imported as a bookmark folder in your internet browser, you can download The bookmark file here by right click ‘save link as’.

R

RESOURCE NAME URL
R Consortium - YouTube https://www.youtube.com/channel/UC_R5smHVXRYGhZYDJsnXTwg/videos
Welcome · Advanced R. https://adv-r.hadley.nz/index.html
Gaston Sanchez http://www.gastonsanchez.com/
BasicBasics 1 : R-Ladies Sydney https://rladiessydney.org/courses/ryouwithme/01-basicbasics-1/
Learning R with humorous side projects - Ryan Timpe https://resources.rstudio.com/rstudio-conf-2020/learning-r-with-humorous-side-projects-ryan-timpe
YaRrr! The Pirate’s Guide to R https://bookdown.org/ndphillips/YaRrr/
tidyverse Data analysis using R https://uomresearchit.github.io/r-tidyverse-intro/
daattali/addinslist: Discover and install useful RStudio addins https://github.com/daattali/addinslist
Swirl courses, learn R in your terminal https://swirlstats.com/students.html
rstudio::conf 2019 videos https://resources.rstudio.com/rstudio-conf-2019
R for Data Science https://r4ds.had.co.nz/
Big Book of R https://www.bigbookofr.com/
Torfs+Brauer-Short-R-Intro.pdf https://cran.r-project.org/doc/contrib/Torfs+Brauer-Short-R-Intro.pdf
R for Excel users - Rex Analytics http://rex-analytics.com/r-for-excel-users/?utm_content=buffer66dd3=social=twitter.com=buffer
Rex Blogs - Rex Analytics http://rex-analytics.com/rex-blogs/

Python

RESOURCE NAME URL
Python Data Science Handbook : Python Data Science Handbook https://jakevdp.github.io/PythonDataScienceHandbook/
The Hitchhiker’s Guide to Python! — The Hitchhiker’s Guide to Python https://docs.python-guide.org/
Interactive Spyder and Jupyter Matplotlib plots in separate window : Michael Hirsch, Ph.D. https://www.scivision.dev/spyder-with-ipython-make-matplotlib-plots-appear-in-own-window/
Data Science from Scratch: First Principles with Python http://math.ecnu.edu.cn/~lfzhou/seminar/[Joel_Grus]_Data_Science_from_Scratch_First_Princ.pdf
Python as a Second Language: Basics https://swcarpentry.github.io/python-second-language/01-basics/
Episodes - [Talk Python To Me Podcast] https://talkpython.fm/episodes/all
Image processing in Python — scikit-image http://scikit-image.org/
Introduction to Cultural Analytics using Python https://melaniewalsh.github.io/Intro-Cultural-Analytics/welcome.html

Data Visualizations

RESOURCE NAME URL
From data to Viz : Find the graphic you need https://www.data-to-viz.com/
Knight Lab https://knightlab.northwestern.edu/
Search for Charts by Data Visualization Functions https://datavizcatalogue.com/search.html
visgap.pdf http://legacydirs.umiacs.umd.edu/~elm/projects/visgap/visgap.pdf
The Xenographic Matrix – Xenographics https://xeno.graphics/the-xenographic-matrix/
Yan Holtz’s material for teaching data analytics and data visualization. https://www.yan-holtz.com/teaching
AutoDraw https://www.autodraw.com/
Chart.js : Open source HTML5 Charts for your website http://www.chartjs.org/
About : RAWGraphs https://rawgraphs.io/about
7 Data Visualization Types You Should be Using More (and How to Start) : by Evan Sinar : Medium https://medium.com/@EvanSinar/7-data-visualization-types-you-should-be-using-more-and-how-to-start-4015b5d4adf2
Zooniverse https://www.zooniverse.org/
Tinkercad : Create 3D digital designs with online CAD https://www.tinkercad.com/
Image analysis for biologists https://www.futurelearn.com/courses/image-analysis

General Data Science

RESOURCE NAME URL
Becoming a Data Scientist – Curriculum via Metromap ← Pragmatic Perspectives http://nirvacana.com/thoughts/becoming-a-data-scientist/
Exploratory Data Analysis Course Notes https://sux13.github.io/DataScienceSpCourseNotes/4_EXDATA/Exploratory_Data_Analysis_Course_Notes.html
Python vs. R: The battle for data scientist mind share : InfoWorld http://www.infoworld.com/article/3187550/data-science/python-vs-r-the-battle-for-data-scientist-mind-share.html
The Architecture of Open Source Applications: VisTrails http://www.aosabook.org/en/vistrails.html
Recommended Resources for Beginners : Data Sci Guide http://www.datasciguide.com/recommended-resources-for-beginners/
ResBaz Tucson May 18-29, 2020 https://researchbazaar.arizona.edu/resbaz/resbazTucson2020/

Git

RESOURCE NAME URL
Front matter · GitBook https://pfern.github.io/OSODOS/gitbook/
github free programming books https://github.com/EbookFoundation/free-programming-books/blob/master/free-programming-books.md#python
Who is this for? · GitBook https://pfern.github.io/OSODOS/gitbook/ROADMAP/
Github for the useR http://happygitwithr.com/
On undoing, fixing, or removing commits in git https://sethrobertson.github.io/GitFixUm/fixup.html
GitHub for Beginners : GitHub Resources Library https://resources.github.com/webcasts/GitHub-for-beginners/
GitHub Guides https://guides.github.com/
Git Tutorial - Try Git https://try.github.io/levels/1/challenges/1
10 Common Git Problems and How to Fix Them - DEV Community 👩‍💻👨‍💻 https://dev.to/citizen428/10-common-git-problems-and-how-to-fix-them-234o
GitHub Doubles Inventory in Learning Lab – Campus Technology https://campustechnology.com/articles/2018/08/06/github-doubles-inventory-in-learning-lab.aspx?s=ct_im_070818=1
Git and GitHub learning resources - User Documentation https://help.github.com/articles/git-and-github-learning-resources/
git - the simple guide - no deep shit! http://rogerdudler.github.io/git-guide/
A Visual Git Reference https://marklodato.github.io/visual-git-guide/index-en.html
Git for Scientists https://milesmcbain.github.io/git_4_sci/
Git and GitHub · R packages http://r-pkgs.had.co.nz/git.html
Understanding Git (part 1) — Explain it Like I’m Five https://hackernoon.com/understanding-git-fcffd87c15a3
Contribute to someone’s repository http://kbroman.org/github_tutorial/pages/fork.html

Linux/Bash

RESOURCE NAME URL
How to Install Ubuntu Linux on VirtualBox on Windows 10 [Step by Step Guide] https://itsfoss.com/install-linux-in-virtualbox/
How To Get Started With The Ubuntu Linux Distro : Gizmodo Australia https://www.gizmodo.com.au/2017/11/how-to-get-started-with-the-ubuntu-linux-distro/
The Unix Workbench http://seankross.com/the-unix-workbench/command-line-basics.html#hello-terminal

High Performance Compute/Cloud Compute

RESOURCE NAME URL
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them https://www.biostars.org/p/63816/
HPC in a day https://swcarpentry.github.io/hpc-novice/
Nectar training http://training.nectar.org.au/
HPC Novice- Softcarp http://swcarpentry.github.io/hpc-novice/
Containers on HPC and Cloud with Singularity https://pawseysc.github.io/singularity-containers/
Open GPU Data Science : RAPIDS https://rapids.ai/
Training Material - User Support Documentation - Pawsey Documentation https://support.pawsey.org.au/documentation/display/US/Training+Material

Machine learning

RESOURCE NAME URL
Machine Learning Version Control System https://dvc.org/
Weka 3 - Data Mining with Open Source Machine Learning Software in Java http://www.cs.waikato.ac.nz/ml/weka/

Tech writing

RESOURCE NAME URL
The Journal of Open Source Software http://joss.theoj.org/about

Data management and Reproducible Research

RESOURCE NAME URL
3. Process - CESSDA TRAINING https://www.cessda.eu/Training/Training-Resources/Library/Data-Management-Expert-Guide/3.-Process
Browse by subject : re3data.org http://www.re3data.org/browse/by-subject/
De-identification - ARDC https://www.ands.org.au/__data/assets/pdf_file/0003/737211/De-identification.pdf
Code Testing — The Turing Way https://the-turing-way.netlify.app/reproducible-research/testing.html
Repeat After Me - by Maki Naro https://thenib.com/repeat-after-me

Dir of tools and repos

RESOURCE NAME URL
Openscience- open source tools by use http://openscience.org/links/
Open Knowledge Maps - A visual interface to the world’s scientific knowledge https://openknowledgemaps.org/
Science https://github.com/showcases/science
Open Knowledge: Projects https://okfn.org/projects/
The Open Data Handbook http://opendatahandbook.org/guide/en/
ckan – The open source data portal software https://ckan.org/
protocols.io - Life Sciences Protocol Repository https://www.protocols.io/
CC Search https://search.creativecommons.org/
Labs and Tools - Nectar https://nectar.org.au/labs-and-tools/
OpenWetWare https://openwetware.org/wiki/Main_Page
About - data.gov.au https://data.gov.au/about
Welcome to the OpenBCI Community · OpenBCI Documentation https://docs.openbci.com/docs/Welcome.html
CVL on Wiener list of software tools : CVL Community https://characterisation-virtual-laboratory.github.io/CVL_Community/FAQs/

Data Reshaping

RESOURCE NAME URL
Tabula: Extract Tables from PDFs http://tabula.technology/
Whiteboard Picture Cleaner - Shell one-liner/script to clean up and beautify photos of whiteboards! https://gist.github.com/lelandbatey/8677901
OpenRefine/OpenRefine Wiki https://github.com/OpenRefine/OpenRefine/wiki/Installation-Instructions#linux

Stats help

RESOURCE NAME URL
5minuteStats http://stephens999.github.io/fiveMinuteStats/index.html
Cross Validated https://stats.stackexchange.com/
Which Stats Test - SAGE Research Methods http://methods.sagepub.com/which-stats-test
Choosing the Correct Statistical Test in SAS, Stata, SPSS and R https://stats.idre.ucla.edu/other/mult-pkg/whatstat/
Learning Statistics with R https://learningstatisticswithr.com/
Statistical Thinking for the 21st Century https://statsthinking21.org/
1 Introduction : A Matrix Algebra Companion for Statistical Learning https://www.gastonsanchez.com/matrix4sl/intro.html

Bioinfo

RESOURCE NAME URL
Bioinformatics Tutorials : Phil Chapman’s Blog https://chapmandu2.github.io/post/2017/11/06/bioinformatics-tutorials/
learn BioInfo - ROSALIND http://rosalind.info/about/
Living in an Ivory Basement http://ivory.idyll.org/blog/
RESOURCE NAME URL
ecocloud : https://ecocloud.org.au/
Free and Open Access to Biodiversity Data : GBIF.org http://www.gbif.org/
SunPy http://sunpy.org/
What is Dr Climate? : Dr Climate https://drclimate.wordpress.com/what-is-dr-climate/
ZoaTrack - Free Animal Tracking Software http://zoatrack.org/
Education : DataONE https://www.dataone.org/Education?ct=t(andsUP_06DEC_2016)
Macroeco: Ecological pattern analysis in Python — macroeco 1.0 documentation http://macroeco.org/
Atlas of Living Australia – Open access to Australia’s biodiversity data https://www.ala.org.au/
TERN - Australia’s Land Ecosystem Observatory : Critical Data https://www.tern.org.au/

Geospatial and Maps

RESOURCE NAME URL
Geospatial data and metadata - ANDS http://www.ands.org.au/working-with-data/metadata/geospatial-data-and-metadata
Getting Started http://docs.qgis.org/2.18/en/docs/user_manual/introduction/getting_started.html
Queensland Globe https://qldglobe.information.qld.gov.au/
Google Maps and R https://www.littlemissdata.com/blog/maps
AURIN Home - AURIN. Australian Urban Research Infrastructure Network https://aurin.org.au/

Humanities, Arts and Social Sciences

RESOURCE NAME URL
All Those Shapes — Google Arts Culture https://www.google.com/culturalinstitute/beta/category/place
Google Arts Culture https://www.google.com/culturalinstitute/beta/
Google Expeditions https://edu.google.com/expeditions/
Humanities Networked Infrastructure - HuNI https://huni.net.au/#/search
Omeka https://omeka.org/
Word Tree / Fernanda Viegas Martin Wattenberg http://hint.fm/projects/wordtree/
Text Mining with R https://www.tidytextmining.com/index.html
PLOS Collections: Article collections published by the Public Library of Science http://collections.plos.org/textmining

IT misc

RESOURCE NAME URL
Atom https://atom.io/
Code Carabiners: Essential Protection Tools for Safe Programming - O’Reilly Radar http://radar.oreilly.com/2014/01/code-carabiners-essential-protection-tools-for-safe-programming.html?cmp=tw-prog-na-article-pr_code_carabiners
Code for a Living - Stack Overflow Blog https://stackoverflow.blog/code-for-a-living/
Hard Coding Concepts Explained with Simple Real-life Analogies https://medium.freecodecamp.org/hard-coding-concepts-explained-with-simple-real-life-analogies-280635e98e37
CodeNewbie https://www.codenewbie.org/learn
GNU Parallel tutorial https://www.gnu.org/software/parallel/parallel_tutorial.html
Web designing tutorial list https://github.com/djunicode/resources
Insights - Stack Overflow Blog https://stackoverflow.blog/insights/

Lessons and books misc

RESOURCE NAME URL
Free Courses Online : Open2Study https://www.open2study.com/courses
Quartz/bad-data-guide: An exhaustive reference to problems seen in real-world data along with suggestions on how to resolve them. https://github.com/Quartz/bad-data-guide#data-are-in-a-pdf
Subjects - OpenStax https://openstax.org/subjects
Random Carpentries https://orchid00.github.io/The_Carpentries_info/carpentries_style_shared_lessons
Open Textbook Library https://open.umn.edu/opentextbooks/subjects/computer-science-information-systems

Cheatsheets

RESOURCE NAME URL
R Cheat Sheet and Guide for Graphical Parameters : FlowingData https://flowingdata.com/2015/03/17/r-cheat-sheet-for-graphical-parameters/
MiscCheatsheets http://practicalcomputing.org/files/PCfB_Appendices.pdf