Resources

I collected some free resources relate to research skills.

Coding

• Python Data Science Handbook by Jake VanderPlas
• R for Data Science by Hadley Wickham & Garrett Grolemund
• Advanced R by Hadley Wickham
• Tidy Evaluation by Lionel Henry & Hadley Wickham
• Mastering Spark with R by Javier Luraschi, Kevin Kuo, & Edgar Ruiz
• SparkPackages for Spark extensions and Maven repository for Java libraries to customize Spark programming
• Learning Apache Spark with Python by Wenqiang Feng
• Intro to R Bayes Packages by Melissa Wong
• R Packages by Hadley Wickham & Jenny Bryan for developing R packages
• Big Book of R by Oscar Baruffa lists 150+ books on R programming
• HackerRank for coding practice in multiple programming languages esp. SQL and Python
• Devpost for some fun online hackathon opportunities

Statistics

• Learning Statistics with R by Danielle Navarro
• The Elements of Statistical Learning: Data Mining, Inference, and Prediction by Trevor Hastie, Robert Tibshirani, & Jerome Friedman
• Geocomputation with R by Robin Lovelace, Jakub Nowosad, & Jannes Muenchow
• An Introduction to Spatial Data Analysis and Visualisation in R by Joshua Menke & William Menke
• Environmental Data Analysis with Matlab by Robin Lovelace, Jakub Nowosad, & Jannes Muenchow
• Forecasting: Principles and Practice by Rob J Hyndman & George Athanasopoulos
• An Introduction to Bayesian Thinking by Merlise Clyde et al.
• VassarStats is a platform that explains statistics concepts (frequentist type) and for online small scale data analyses
• JPSP is an open source statistics program that’s similar to SPSS, but with additional Bayesian analyses options
• Bernard Marr a listserv for trends in Big Data & Analytics

Data Visualization

• Fundamentals of Data Visualization by Claus O. Wilke
• The Visual Display of Quantitative Information by Edward R. Tufte
• Adobe Color Wheel for finding color match and then use the color code in other visualization tools eg., Tableau
• R Graphics Cookbook by Winston Chang
• R Graph Gallery for different figure templates in R
• Matplotlib Gallery for figure templates in Python
• D3 Gallery
• Mastering Shiny by Hadley Wickham (Shiny is a popular data app)
• From Data to Viz helps match graph types to data types
• FURY a Python library for scientific visualization

Modeling

• Neuromatch Acadmy Course Materials
• Neurohackademy Course Videos through UW eScience Institute
• Machine Learning Summer Schools Lecture Videos in the past years
• Foundations of Machine Learning curriculum slides and code for core machine learning concepts
• Tidy Modeling with R by Max Kuhn & Julia Silge
• Text Mining with R by Julia Silge & David Robinson
• A Minimal rTorch Book by Alfonso R. Reyes
• Feature Engineering and Selection: A Practical Approach for Predictive Models by Max Kuhn & Kjell Johnson
• Feature Engineering for Machine Learning by Alice Zheng & Amanda Casari
• Pattern Recognition and Machine Learning by Christopher M. Bishop
• Deep Learning by Ian Goodfellow, Yoshua Bengio, and Aaron Courville
• Neural Networks and Deep Learning: Introduction to core principles by Michael Nielsen
• Information Theory, Inference, and Learning Algorithms by David Macay
• Machine Learning Crash Course by Google
• Interpretable Machine Learning A Guide for Making Black Box Models Explainable by Christoph Molnar
• Bayes Rules! An Introduction to Bayesian Modeling with R by Alicia A. Johnson, Miles Ott, & Mine Dogucu
• Reinforcement Learning: An Introduction by Richard S. Sutton & Andrew G. Barton
• Kaggle for downloading some fun public datasets to try out machine learning algorithms

Cloud Computing

• AWS EC2 cloud-based compute instance and AWS S3 cloud-based object storage tutorials
• AWS Open Data for Neuroscience: International Neuroimaging Data-Sharing Initiative (INDI), OpenNeuro, Open NeuroData, Allen Brain Observatory, The Human Connectome Project, NYU Langone & FAIR FastMRI Dataset
• Publicly Available Pre-configured Machine Images on Google Cloud
• brainlife a free cloud platform for secure neuroscience data analysis

Neuroscience - General

• Functional Neuroanatomy for an introduction to neuroanatomy with virtual brain dissection
• The INCF Training Space contains videos of lectures and tutorials of using computational neuroscience tools
• Neuroscience Gateway (NSG) gives neuroscientists free access to High Performance Computing resources
• EBRAINS gives researchers access to shared and curated open data (including the Human Brain Project data)
• Allen Institute’s The Virtual Science Lab teaches researchers how to use open data from Allen Institute in class
• BrainFacts.org for fun facts of the human brain (The book Brain Facts is also the guide book for Brain Bee events)
• Increasing Women in Neuroscience (IWiN) interactive courses, toolkits, and related resources
• Environmental Psychology lectures by Prof. Daniel Stokols

Neuroscience - MRI imaging processing

• A simple but useful way to assess fMRI scan qualities an effective first-step to check your fMRI data
• fMRI Bootcamp introduces main methodologies in fMRI data analyses by Rebecca Saxe
• DIPY workshop training videos given by DIPY developers for DTI (diffusion tensor imaging) analysis
• NiMARE a Python package for neuroimaging meta-analysis
• Nobrainer provides a deep learning framework for 3D image processing and pre-trained models for brain extraction, brain segmentation, brain generation, etc.
• Nitime a Python package for time series analysis in neuroscience
• Mindboggle a platform that takes in preprocessed T1-weighted MRI data and outputs different types of brain morphometry
• Neuroscience Workflow Systems: Nipype, Pydra, snakemake, Nextflow
• PySurfer for visualizing human brain
• WagnerLabPapers for python codes used to generate fMRI figures in journals

Academic Writing

• The Writing Workshop by Barbara Sarnecka
• ProWritingAid or Grammarly for copy editing
• Mendeley or Zotero for managing and citing literatures
• Purdue Online Writing Lab for APA format
• papaya - an R package for creating APA style manuscript using Rmarkdown
• Overleaf for creating documents using LaTeX (different journal templates available, including IEEE)
• Websites for preregistration: Open Science Framework (OSF), ClinicalTrials.gov, AEA RCT Registry, egap, RIDIE, Research Registry
• Power Writing - a newsletter on writing tips that updates every Tuesday by Daphne Gray-Grant

Presentation & Science Communication

• a nature article on how scientific presentation is different from a journal article
• Design for an Audience by a science graphics editor of The New York Times
• Morrison billborad poster - an award-winning poster format that applies modern principles of graphic design and user experience research (template downloadable)
• Kapwing for caption recorded videos or Google Slides - Caption for caption presentation in real time
• Activate to Captivate a monthly newsletter that gives tips on communication skills by Bri McWhorter
• ComSciCon - a series of workshops on science communication
• SCOPE (Science Communication Online Programme) hosted by Northwestern University
• xkcd Simple Writer a fun app that tells when the words you use aren’t listed in the top 1000 most common words

Peer Review

• Focus on Peer Review - a free Nature Masterclasses’ online course on peer review process
• Elsevier Researcher Academy provides courses to understand the publishing process (including review)
• Scholarly Peers a collection of resources for supporting researchers engaging in the peer-review process, as authors, reviewers, and editors. The group is also available for questions on Twitter @scholarly_peers
• an article on How to Criticize with Kindness: Philosopher Daniel Dennett on the Four Steps to Arguing Intelligently

Interdisciplinary Collaboration

• Toolbox Dialogue Initiative research and outreach collective for interdisciplinarity by Michigan State University
• td-net toolbox methods and tools for co-producing knowledge by Swiss Academy of Sciences

Time Management

• Online Pomodoro
• Appointment systems with free service YouCanBook.me, Square Appointments, SimplyBook.me

Professional Development

• Cultivating Relationships suggestions for contacting professors
• Finding your research home a 15-min video with great tips on finding a suitable lab from NIH Training & Education
• Guide to Cover Letters from NIH
• Requesting Letters of Recommendation suggestions for requesting letters of recommendation
• The Professor Is In a blog about navigating different stages of academic career
• The Quick and Relatively Painless Guide to Your Academic Job Search by Dr. Karen Kelsky
• Academic Application Materials from UCI Division of Career Pathway
• Letters to Young Scientists Science Careers’ column with insightful suggestions to professional development
• Prof. Brad Voytek’s Lab Philosophy about mentorship, grades, imposter syndrome - very inspiring
• MindTools Toolkits for developing skills including time management, leadership, communications, etc.
• The Batch gives you a weekly fresh taste of the latest research and applications in the field of AI by Andrew Ng
• xcorr: comp neuro a blog about computational neuroscience, data science, getting into industry by Patrick Mineault
• Tanya Jonker a blog about academic and industry job markets by cognitive neuroscientist Tanya Jonker
• Cheeky Scientist a platform that guides PhDs into industry career