awesome-PhD

A curated list of carefully selected tools and resources I wish I knew when starting my PhD. All of these tools make your life SO MUCH easier and are both for early career as well as more senior researchers (or even if you are not in academia, for that matter). The original Twitter thread where I started this list can be found here.

This repository is aimed to be a living, constantly developing resource where everybody can contribute with new resources! If you want to contribute, please read the contribution guidelines here first, then send a pull request or contact me on Twitter in case of any questions.

Table of Contents

• Other (awesome) lists on this topic
• List of resources
  • Analysis
  • Career
  • Crediting
  • Data
  • Design
  • Events
  • Inclusion
  • Infographics and Cheatsheets
  • Keyboard shortcuts
  • Literature
  • Meta-analyses
  • Miscellaneous
  • Networking
  • Neuroscience
  • Online presence
  • Organization
  • Podcasts
  • Publication
  • References
  • Reproducibility
  • Stimuli
  • Version control
  • Visualization
  • Writing
• Special thanks for contributions to this list

Other (awesome) resources on this topic

• ARIADNE from IGOR - a scientific resource collection to navigate the resource jungle.
• Awesome AI Research Tools by Iman Reihanian - a curated list of AI tools for the research workflow: literature review, paper Q&A, citation management, writing, and open datasets.
• awesome-phd by Alireza Samar.
• awesome-phd-advice by Paul Liang.
• Doctoral Student Cheat Sheet by Justin Harty.
• PhD Resources by Guillaume Dalle
• Resources for Postdocs by Lei Zhang.

List of resources

Sorted alphabetically into sub-categories.

Analysis

• DATAPASTA: This R package is "about reducing resistance associated with copying and pasting data to and from R". Copy data from Excel and paste it into R as a dataframe or tibble.
• METAFOR: Use the metafor package in R for your meta-analyses.
• STATCHECK: To check a PDF, DOCX or HTML file for errors in statistical reporting, upload it to Statcheck. Some journals even officially request this now (e.g., Psychological Science).
• WEB PLOT DIGITIZER: Helps you to reverse engineer data from visualizations by extracting the underlying numerical values.

Career

• JOB INTERVIEW: Jonathan Birch gives some helpful tips on how to navigate tenure-track job talks.
• PHD COMPETENCE MODEL: This is "a self-assessment tool to help PhD candidates more efficiently direct their time towards improving skills areas that are most needed for their own personal career development."
• POSTDOC FUNDING: Find a list of postdoctoral funding opportunities (there are also separate lists for neuroscience/neurology and cancer/oncology).
• SIGMACV: A free, open-source tool that auto-builds your academic CV from ORCID and OpenAlex — curate it and export to PDF, Word, LaTeX or Markdown, or publish a living public page.
• TALK INVITATIONS: Have you been invited to speak somewhere? Here are some questions you might (and should) ask beforehand.

Crediting

• CITATION DIVERSITY STATEMENT: To increase awareness about citation bias and mitigate it, by checking for and transparently reporting proportions of citing male and female first and last authors, use the citation diversity statement by Zurn et al. (2020, TICS).
• CITATION GECKO: "Gecko is here to help you find the most relevant papers to your research and give you a more complete sense of the research landscape."
• CREDIT AUTHOR STATEMENT: Use the CRedit Author Statement by Brandt et al. (2015, Learned Publishing) to report each author’s proper contribution to a manuscript.
• TENZING: Use the Tenzing ShinyApp for quickly and easily documenting contributorship.

Data

• 24 DAYS OF DATABASES: Somebody on twitter was gracious enough to summarize some cool datasets that you can work on.
• POPANE DATASET: A large database on the psychophysiology of positive and negative emotions. "This database involves recording of 1157 healthy participants, collected across seven studies, a continuous recordof self-reported affect along with several biosignals (electrocardiogram, impedance cardiogram, electrodermal activity, hemodynamic measures, e.g., blood pressure), respiration trace, and skin temperature. [The authors] experimentally elicited a wide range of positive and negative emotions, including amusement, anger, disgust, excitement, fear, gratitude, sadness, tenderness, and threat".

Design

• SAMPLE SIZE JUSTIFICATION: If you need help justifying your sample size, use this Shiny app from Daniel Lakens.

Events

• OPEN RESEARCH CALENDAR: Keep up with all events related to open scholarship with this handy calendar. You can also follow them on Twitter here.
• REPRODUCIBILITEA: Want to discuss the latest papers related to open scholarship? Have a look whether there already is a Reproducibilitea journal club at your institution, and if not, create one of your own!
• RIOT SCIENCE CLUB: The RIOT Science Club is organizing amazing events related to open scholarship. Also visit their Youtube channel for all the recorded talks.

Inclusion

• COLS4ALL: An R package "for selecting color palettes. 'Color for all' refers to [the authors'] mission that colors should be usable for not just people with normal color vision, but also for people with color vision deficiency".
• EQUITY COMPASS: A great free online course called "Equity in Informal STEM Learning: Using the Equity Compass" on how to be more inclusive.

Infographics and Cheatsheets

• CHOOSE YOUR PLOT: No idea how to best plot your data? Have a look at this image.
• DOWNLOAD SCIENTIFIC PAPERS: Many roads lead to you being able to read a scientific paper...check your options in this handy flowchart.
• ETYMOLOGY OF THE BRAIN: Want to know how some parts of the brain got their names? Check out this cool image.
• fNIRS CHEATSHEET: A hitchhiker's guide to fNIRS data analysis for beginners.
• GITHUB CHEATSHEET: Confused by commit, stage, stash, fetch, etc. on GitHub? Here's the sheet for you.
• JUPYTER NOTEBOOK CHEATSHEET
• R CHEATSHEETS: There are loads of cheat sheets to help you find your way around in R.

Keyboard shortcuts

• Use Windows key + Shift + S to take a cropped screenshot

Literature

• CODA: Use Coda, a machine-readable history of cooperation research, to search, select and visualize studies for on-demand meta-analysis.
• CONNECTED PAPERS: To explore connections between published papers (e.g., for a literature review), use Connected Papers. This is also nice to see the reach of your own research! It is a "unique, visual tool to help researchers and applied scientists find and explore papers relevant to their field of work".
• CONSENSUS: A search engine that uses AI to extract and summarize findings from scientific work.
• COVIDENCE: This paid tool is well worth its money, because it helps you screen and decide on hundreds of papers if you're working on a systematic review.
• ELICIT: Elicit is your AI research assistant that "uses language models to help you automate research workflows", by finding "relevant papers without perfect keyword match", summarizing "takeaways from the paper specific to your question", and extracting relevant information.
• LITERATURE EXCEL SHEET: No literature review will ever be the same again, if you use this tutorial to organize all your literature in Excel.
• LITERATURE TRACKER: Have a look at this useful tutorial to keep your literature organized.
• LITMAPS: An all-rounder tool for visual research navigation, citation network search, and team synchronization.
• RESEARCH RABBIT: Use Research Rabbit to find both germinal and future works from a single (or multiple) works.
• SCHOLARCY: Want an AI to summarize literature for you? Wait no more, Scholarcy comes to the rescue.
• SCITE: A platform for evaluating scientific articles via smart citations, which allows users to assess how a publication has ben cited.
• SEABOAT: This app helps you organize your evaluation of a empirical research, focusing on threats to validity. Read the corresponding paper .