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 rightclick ‘save link as’.
Hacky Public
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 |
| 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 |
| 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/ |
Eco/Enviromental links
| 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 |