Links
RNA-seq
- OmicsML/awesome-deep-learning-single-cell-papers
- P and q values in RNA Seq
- FastQC A Quality Control tool for High Throughput Sequence Data
- Basics of Single-Cell Analysis with Bioconductor
- Single-cell best practices
- Random Survival Forests
- PCA
- UMAP
- How can t-SNE or UMAP embed new data
- Drawing Transformer Network
- Visualization of RNA-Seq results with Volcano Plot
- Volcano
- Heatmap
trajectory analysis
- Monocle
- velocyto
- kallisto | bustools
- mRNA splicing: 40 years on
- How fast do RNAs and proteins degrade?
Spatial omics
- Visium HD spatial datasets with Seurat
- Visium HD to cell
- H&E to Xenium DAPI Image Registration with Fiji
- Microscope Image Compatibility with Space Ranger
- Tumor-infiltrating lymphocyte (TIL) therapy
- Cell Image Library
AI & Algorithms
- Deep Learning Book
- Variational inference
- L1 and L2 regularization
- Overfitting in Machine Learning
- The 5 Levels of Machine Learning Iteration
- Bias/Variance and Model Selection
- Convolutional Neural Networks for Visual Recognition
- Vision Transformers (ViT) Explained
- LLaVA
- Stable Diffusion
- What are Diffusion Models? | Lil’Log
- Quantify similarity between time series
- The Unreasonable Effectiveness of Recurrent Neural Networks
- Peak signal detection
- Shapley Values
- Democratising Knowledge Graphs — BioCypher
Computer environment
- Add Conda environment to jupyter notebook
- Singularity-tutorial.github.io
- Huggingface environment variables