Useful Links
January 10, 2023 ยท View on GitHub
I got tired of bookmarking everything I found useful in my browser, so here's an organized list of stuff I think is useful/cool.
TABLE OF CONTENTS
GENERAL SCIENCE
- Software Carpentry
- Biorender
- Semantic Scholar
- XSEDE: Good way to get compute time if you don't have an HPC but need the resources
- Inkscape: draw pretty pictures
- How to Write a Scientific Review Article
- Overleaf
- An extremely clear and concise way to communicate when reviewing/commenting on something
- One of the best set of bulletpoints for effective team management I've seen
- Erik Anderson's lab has an excellent example "Dry Lab Guide"
NGS
- Bioinfo Courses/Books
- Tommy Tang's one liners
- Bioinformatics course, covers most of the basics
- Great list of textbooks for bioinformatics
- EMBL Tutorials: lot of great walkthroughs, some specific to EMBL-EBI, some not
- Biostars Tutorials: Did you know biostars isn't just a site for asking the same question about what the SAM bitflag field means for two decades?
- Biostars Handbook: Where you can read about what the SAM bitflag field means without asking some postdoc trying to procrastinate their work
- Genomics Workflows on AWS
- Snakemake
- More Snakemake
- RNA Seq Workflow with Snakemake
- Real Time Genomics Tools: Some neat simulation tools and other stuff
- Mike Love RNA seq twitter thread
- UCSC List of tools
- Excellent workflow language tutorial
GENERAL PROGRAMMING
- Guide to Scientific Programming Reproducibility
- Docker
- A Guide to Good Research Code
- How to think like a computer scientist
- A Cloud Guru
- VSCode Keyboard Shortcuts
- github1s: Lets you use VSCode in a browser to see github repos
- ChooseALicense
- Rstudio Cloud
- Markdown2Pdf
BASH
- Terminal-based delimited data tool
- Automation and Make
- Vim Cheat Sheet
- Regex Crossword
- glogg
- crontab guru
- Pandoc: a very useful document conversion tool
PYTHON
- PEP8: Python style guide
- black: an autoformatter for when you're too lazy to read PEP8
- Multiprocessing Guide
- Conda
- Dash: the Python equivalent to Rshiny
MACHINE LEARNING
- ML Notebooks
- Python Data Science Handbook
- Graph of classification accuracy metrics
- Neural Network SVG Generator
- Keras
- scikit-learn
- 9 Tools I wish I had learned before my PhD in Machine Learning
- DL2AI
- Goodfellow Deep Learning Book
- Excellent slides on Time Series Forecasting