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

• soon to be released: ARIADNE from IGOR - a scientific resource collection to navigate the resource jungle.
• 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).
• 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 here.
• SEMANTIC SCHOLAR: A free, AI-powered research tool to find scientific literature.
• SNOWBALL: A tool that would find related articles with snowballing method.

Meta-analyses

• 10 EASY STEPS: A tutorial paper on "10 easy steps to conducting transparent, reproducible meta-analyses for infant researchers".
• METALAB: This website features interactive, community-augmented meta-analysis tools for cognitive development research.
• TEMPLATES: A primer and tutorial paper on "Conducting a meta-analysis in the age of open science: Tools, tips, and practical recommendations", including nine templates free for use, from preregistration to code to data.

Miscellaneous

• COLOR CONVERTER: If you need to find out the code for a certain color, check this handy converter.
• DATA HORROR ESCAPE ROOM: Solve cool puzzles together and learn more about all the horrors data has to offer.
• OPEN SCIENCE ESCAPE ROOM: Want to playfully learn about open science? Check out this fun online escape room.
• SEMANTIC SCALE NETWORK: If you want to create a new scale but are not sure whether it exists already, check the Semantic Scale Network to detect semantically related (psychological) scales. You can also add your own scales in there to extend the database.

Networking

• ACADEMICS ON MASTODON: A list of various lists consisting of academics on Mastodon and general guidance for academic use.
• TWITTER FOR SCIENTISTS: A handy guide on how to start off on Twitter if you're a scientist.

Neuroscience

• 3D BRAIN: Do you have an anatomical scan of your brain and access to a 3D-printer? Follow this easy tutorial to print your own brain.
• DICOMTAGS: Do you want to know where a specific information is saved in the DICOM file of your imaging data. Check out DICOM Tags.
• EDUCORTEX: This handy educational, browser-based visualization tool allows you to enter any functional or anatomical term and visualize the parts of the brain that are most associated with that term. Check the GitHub repository or corresponding paper.
• FMRI COURSE: Learn how to design and analyze fMRI experiments in this free course.
• NEUROQUERY: NeuroQuery is a tool for meta-analysis of neuroimaging studies, relating text queries to activations as well as associations between terms used together in neuroimaging publications. More info in the corresponding paper.
• NEUROSYNTH: NeuroSynth is for large-scale, automated synthesis of functional magnetic resonance imaging (fMRI) data. You can search for word associations and papers with specific MNI coordinates.

Online Presence

• WOWCHEMY WEBSITE: If you want to create your own website, but have no clue where to start, check out Daniel Quintana's extremely easy tutorial! Also have a look at my website for an example.

Organization

• BRAINVERSE: A neat, open-source, cross-platform tool for notetaking, experiment planning and a labbook tool.
• NOTION: I've said it before and I'll say it again - Notion is the best application there is to keep all your (PhD) note-taking mess in one place. If you want to save Tweets and Threads automatically to Notion, use this tutorial.
• TRELLO: Trello helps you stay organized and work together with others by letting you create lists about anything you want.
• The Good Research Code Handbook: Organize your code so that it is easy to understand and works reliably.

Podcasts

• ACROSS THE AGES: An English podcast delving "into the history of a chosen subject, spanning from way back when, all the way up to some time ago".
• BRAINFLICKS: A German podcast about psychology in movies.
• DEAR GRAD STUDENT: An English podcast "to celebrate, commiserate, and support one another through grad school".
• EVERYTHING HERTZ: An English podcast about methodology and scientific life.
• HONEST ACADEMIA: An English podcast from two grad students discussing navigating academia.
• PLANTHROPOLOGY: An English podcast "about humans who love plants & why you should love plants too".
• SCIENCE SHEROES: A German podcast about women and non-binary people in science.

Publication

• 10 WAYS TO FIND OPEN ACCESS ARTICLES curated by Aleksandra Lazic.
• EDITOR: Have a look at this Twitter thread by Michael Breakspear on his experience as a scientific editor.
• JOURNAL-AUTHOR-NAME-ESTIMATOR: If you don’t know who to suggest as a reviewer or what journal to submit your paper to, check out JANE.
• JOURNAL RATER: If you want to know about the review process and manuscript handling, check out the Journal Rater by PhD Voice. Because “life’s too short to put up with Reviewer 2’s”.
• JOURNAL SUGGESTER: Just paste your abstract and get some suggestions for journals you can submit to.
• ORCID: Get an ORCID - an "Open Researcher and Contributor ID" which is a persistent digital identifier that you own and control, and that distinguishes you from every other researcher. Link your projects and output to your ORCID.
• PUBLONS: Use Publons to keep up with all your peer-reviews and publications - it can also be linked to your ORCID.
• SCIREV: If you want to know how long the review process for a specific journal is, or people's experience with publishing there, check SciRev.
• SHERPA ROMEO: If you are not sure whether you are allowed to upload a preprint prior to journal submission.
• UNPAYWALL: As an alternative to SciHub, consider Unpaywall.

References

• BIBTEX: Bibliography & reference generator that works quite well with Rmd/Papaja.
• CITING R PACKAGES: Here and here are some handy tutorials on how to cite all your used R packages in an RMarkdown document at once. If you want to generate R package citations, look here.
• GRATEFUL: Use the grateful package in R to automatically create a reference list for all your used R packages.
• RECITEWORKS: To check your in-text citations and reference lists for errors, use Reciteworks.
• REFERENCE MANAGEMENT COMPARISON: If you are not sure which reference manager to use, check this handy comparison of all the different ones available and whether they will work on your operating system.

Reproducibility

• NEUROIMAGING: A free online video-based workshop on how to conduct reproducible neuroimaging.
• PREREGISTRATION TEMPLATES: A list of available preregistration templates.
• WORKFLOW: Make your whole workflow more reproducible with this great and free 2-hour workshop.

Stimuli

• EMBODY/EMFACE: This is a 2022 published tool to measure how good people can recognize emotions in the body or face.
• EMPATHY FOR PAIN: Pictures showing hands in painful situations that can be used to assess empathy for others' pain. Find the corresponding paper here.
• FULL BODY STIMULI: Need some full-body stimuli in your experiments? Look no further.
• KAPODI STIMULI DATABASE: A huge database of every emotional stimuli you can think of and may want to use in your experiments.

Version control

• DIFFCHECKER: To compare two files (text/image/PDF/excel) to find the difference between them.

Visualization

• AUTODRAW: AutoDraw magically makes your doodles into nicer graphics by suggesting shapes based on what you drew.
• BIOICONS: A free alternative to BioRender.
• BIORENDER: The all-in-one tool for research visualization in a free and paid verson. Visualize study designs and results, or even design whole posters using their tools and icons.
• BRAIN CODE SELECTOR: This tool summarized tools to visualize brain data in R, Python, and Matlab.
• CANVA: Canva is amazing for creating content such as slides, figures and there are so many great (and free!) designs to choose from.
• COLOR ORACLE: A piece of software that helps you tell whether your plot or slide is accessible to folk with different colour vision impairments.
• COLOR PICKER: Upload an image and pick the hex code of any color in the image.
• FLATICON: Flaticon has a huge amount of free stickers and icons, ready to download and use.
• FONT AWESOME: Font Awesome has loads of free icons to choose from to use in presentations, posters, etc.
• FSBRAIN: This R package "helps visualize surface-based brain structure data for large groups of subjects with very little code" and "also supports the computation of simple brain morphometry measures".
• GANTTRIFY: Check out this handy tool to create Gantt charts in R.
• GGHELP: An R package that "converts a natural language query into a 'ggplot2' command string".
• GGPLOT TRICKS: Some tricks from the R people to level up your ggplot game.
• MIRO: You can use Miro for creating visual presentations of anything, and most of all, for collaboration with others! The possibilities are endless.
• PHYLOPIC: An open database of freely usable silhouettes of life forms.
• R VISUALIZATION: This is a great syllabus about visualizing data in R, held by Claus Wilke.
• MAKE YOUR OWN SCATTERPLOT: This handy tool allows you to draw in scatterplot points and download a CSV file with the coordinates.
• R GRAPH GALLERY: A collection of charts made with the R programming language.

Writing

• ACRONYMIFY: If you need a cool and catchy acronym for your paper, project, etc. check out Acronymify.
• APA-STYLE WORD DOCUMENT: Thanks to Nicolás F. Narvaez Linares for telling me about the readymade APA-style word document option, where you can directly initialize the right formatting in Word.
• LEADERSHIP LAB: If you want to know how to write effectively, watch this video.
• LIST OF ACRONYMS MAKER: Don't waste time collating a list or table of abbreviations manually. This tool does it for you.
• PAPAJA: If you want to create reproducible manuscripts including tables directly from your data in R, use the papaja package.
• PREPRINT TEMPLATES: Amazing and useful "Word templates for typesetting preprints. Because your preprint should be a #prettypreprint" and we don't have time for endless formatting.
• QUILLBOT: Paraphrase like the awesome boss you are using QuillBot.
• THE CRAFT OF WRITING EFFECTIVELY: An effort to communicate helpful rules, skills, and resources that are available to graduate students interested in further developing their writing style.

Special thanks for contributions to this list

• Lei Zhang
• #AcademicTwitter