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List of Spatial Transcriptomics related Tools organized per category
code for "Continuous Hierarchical Representations with Poincaré Variational Auto-Encoders".
Notebooks to follow along with "Deep Learning for Biology" Chapters 2 to 6.
List of software packages for multi-omics analysis
CM et TD de programmation C pour le Master 2 GENIOMHE
Probing metabolomic profile of breast cancer combined with protein expression via machine learning approach
multiNetX is a python package for the manipulation and visualization of multilayer networks. It is build on NetworkX
Friends don't let friends make certain types of data visualization - What are they and why are they bad.
An R package containing example data sets for metabolomics analyses
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎
Python code for the implementation the intuitive method to plot Boolean network attractors landscape
📊 An infographics generator with 30+ plugins and 300+ options to display stats about your GitHub account and render them as SVG, Markdown, PDF or JSON!
SenePy is a set of tools to score single-cells based on their expression of cell-specific senescence markers. Please see the following publication By Sanborn MA et al in Nature Communications (2025…
Workshops presented by the Gladstone Bioinformatics Core
Mapping DEGs to PPI Networks, Identifying Network Hubs and Highly Connected Proteins, and Simulating Genetic Circuits. An End-to-End DIY Guide
Module for embedding igv.js in an IPython notebook
A Python package for handling and visualizing GWAS summary statistics. https://cloufield.github.io/gwaslab/
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Foundation Models for Genomics & Transcriptomics