Resources
Integrated Development Environments
IDE are essential tools for developers, offering a range of features that facilitate coding, debugging, and project management.
Visual Studio Code
Visual Studio Code (VS Code) is a highly popular, open-source code editor developed by Microsoft. It supports a wide range of programming languages and comes with features like IntelliSense code completion, debugging tools, Git integration, and a vast marketplace for extensions.
PyCharm
PyCharm is another IDE from JetBrains, specifically designed for Python development. It provides features like code analysis, graphical debugging, and an integrated terminal. PyCharm also supports web development with Django, Flask, and other frameworks.
Rstudio
RStudio is a powerful and widely-used Integrated Development Environment (IDE) designed to enhance productivity in coding, data analysis, and visualization, primarily for R but also supporting Python. It is the go-to choice for over 90% of R programmers, making it the de facto standard in the field.
Plots and figures
packages and websites that will allow you to easily create stunning figures.
R
ggplot2
A leading data visualization package that implements the Grammar of Graphics, making it easy to create complex plots from data in a data frame.
plotly
An interactive graphing library that makes interactive, publication-quality graphs online.
Python
Matplotlib
Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations.
Seaborn
A statistical data visualization library based on Matplotlib that provides a high-level interface for drawing attractive and informative statistical graphics.
Web sites
From data to Viz
Find the most appropriate graph for your data with great examples and code in R and Python.
Pipelines tools
The best workflows to create analysis pipelines.
Snakemake
Workflow management system that uses a Python-based syntax to create reproducible and scalable data analysis pipelines, making it particularly accessible for users familiar with Python.
Nextflow
Workflow management system that utilizes a domain-specific language based on Groovy, enabling seamless integration of various programming languages and providing robust support for parallel and distributed computing environments.
Web applications
A list of packages and websites to create web applications for your pipelines and scripts.
Shiny
A web application framework for R or Python that can be used to build interactive web applications.
Dash
Dash is the original low-code framework for rapidly building data apps in Python.
Flask
Web application framework designed to make getting started quick and easy, with the ability to scale up to complex applications.
Material
Databases, courses and more.
Glittr
Web application framework designed to make getting started quick and easy, with the ability to scale up to complex applications.
Data & ML
Database
A collection of 200 real-world data science and machine learning case studies across companies.
What statistical test to do ?
A guide to choose the right statistical test to do with your data. Part of an amazing blog about statistics.
Fundamentals of Data Visualization
A complete guide about what to do and not to do when creating figures. And more !
Machine learning, deep learning and LLMs
Links to tutorials or projects for the analysis of genomics data using ML
Toolbox
Diverse tools that will help you handle or analyse your data.
GenoVi
GenoVi generates circular genome representations for complete, draft, and multiple bacterial and archaeal genomes.