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commawesome


Tools, tips, & resources for STEM students/researchers

Getting started

Below is a list of resources relevant to any STEM student/researcher.

(This list is a fork from the resources compiled by fellows at the MIT BE Communication Lab)

This list compiles resources to transform data into a clear message through:

  • data analysis and visualization,
  • figure design,
  • writing and reference management,
  • design tools and resources,
  • professional resources.

It also includes resources for reproducibility and miscellaneous tools for engineering research

Legend

Symbol Meaning
πŸ†“ no upfront cost
πŸ”“ open source
πŸ’΅ small cost
πŸ’° large cost
πŸ“¦ Computing Package
πŸ“š Resource

Computing

Programming

Students typical use the follow resources to analyze and plot data for class and research purposes.

  • Python πŸ†“ πŸ”“ – general applicability, open-source; commonly used with Anaconda, a package and environment manager

  • R πŸ†“ πŸ”“ - popular for bioinformatics, genomics, statistics; typically used with RStudio πŸ†“ using packages from CRAN

    • RStudio introduction to R - a good place to start for complete beginners.
    • Swirl teaches R within RStudio. A great interactive resource for beginners.
  • MATLAB πŸ’° - commercial computing environment offered at MIT for affiliates. See Gnu Octave for an open source πŸ”“ alternative.

  • Other computing languages/platforms used include Julia and Go, but their user bases are much smaller.

Data Visualization

Data Visualization Resources

Plotting Tools

Python Plotting

  • matplotlib – the most popular plotting framework
  • Pandas - table management
  • bokeh – interactive web-based visualization
  • seaborn – opinionated plotting framework for statistical visualizations
  • plotly – interactive web-based visualization
  • altair – straightforward visualization framework, biased towards statistical plotting
  • Rpy2 - use R code in jupyter notebook
  • BECL notes - BECL-produced resource for python related plotting and getting started.

R Plotting

This is an opinionated summary of key tools for plotting in R, focusing primarily on the tidyverse group of packagesπŸ“¦.

  • ggplot2πŸ“¦πŸ”“ – the most popular plotting framework based on the book, Grammar of Graphics
  • plotlyπŸ“¦πŸ”“ – commercially supported interactive web-based visualization tools
  • ShinyπŸ“¦πŸ”“ – interactive charts and applications on the web, great for displaying public data and generating publication website
  • reticulateπŸ“¦πŸ”“ - interface with Python via R
  • ggplot2 Cheatsheet sheetπŸ“š - quick overview of ggplot2 plotting functions and aesthetics
  • ggplot2 TutorialπŸ“š - Harvard tutorial on getting started with ggplot2
  • R Graph GalleryπŸ“š - gallery of plots generated using R
  • R for Data ScienceπŸ“š - a comprehensive resource to become proficient at using R for all data science needs, written by lead instructors at RStudio

Other Plotting tools

  • RAW – fast, easy graphs from Excel or CSV files
  • Graphpad Prism – stand-alone plotting program
  • Excel – the one and only
  • Datawrapper – fast, easy graphs from Excel or CSV files
  • Octave – Free version MATLAB
  • WebPlotDigitiazer

Reproducible Analysis

General Principles

R workflows

  • drake πŸ“¦ – toolkit to build reproducible workflows that scale
  • rapport
  • knitr - allows to convert markdown, R, and plots/tables to html or PDF files, similar to Jupyter for python
  • workflowr
  • here - makes it easy for users to set directories and paths
  • ROpenSci

Python workflows

Scientific Communication

Writing Papers

Writing Tools

LaTeX

Markdown

  • Pandoc - for switching between .doc/.tex/.md/etc file types
  • Microsoft Word

Citations and Reference Management

  • Zotero πŸ†“ πŸ”“
  • Mendeley πŸ†“
  • EndNote πŸ’΅
  • Papers πŸ’΅
  • Readcube
  • Jabref

Figures

Drawing

Image Manipulation

  • Adobe Photoshop πŸ’°
  • Affinity Designer πŸ’΅
  • GIMP πŸ†“ πŸ”“ The GNU Image Manipulation Program
  • ImageJ/Fiji πŸ†“ πŸ”“

Design Tools & Resources

Color

Fonts & Typography

Icons

Images

  • Unsplash - downloadable high-quality images

Poster Design

Poster Design Tools

  • Adobe Illustrator πŸ’°
  • Inkscape
  • Microsoft Powerpoint πŸ’©
  • Adobe InDesign πŸ’°

Poster Templates

Poster Galleries

Professional Resources

Miscellaneous & Unsorted

License

CC0

To the extent possible under law, MIT BECL has waived all copyright and related or neighboring rights to the compilation of this list, but not the resources included.