Stars
VIP cheatsheet for Stanford's CME 295 Transformers and Large Language Models
A growing collection of bioinformatics tutorials, project guides, tools, and articles I’ve developed to make bioinformatics more accessible.
Lab materials for the University of Washington course Data Science for Biologists (Winter 2019, BIO419/519)
Data Analysis with Bootstrapped ESTimation
Jupyter notebook showing how to use pandas to parse JSON data from REST API into dataframes, clustering based on column names and values within the columns as wells as plotting the resulting heatma…
A community shared resource of Python and R Notebooks that utilize the cBioPortal API for various analysis recipes
Course materials for Computational Biology and Bioinformatics - BI462
View a spectrum of dimensionality reduction embeddings for your single-cell data ranging from t-SNE like to UMAP like
Contrastive neighbor embeddings
https://www.sc-best-practices.org
Repository for An Introduction to Applied Bioinformatics built notebooks.
Workshop on advanced python lead by Sergio Netotea
Single cell RNA sequencing analysis course
BioBombe: Sequentially compressed gene expression features enhances biological signatures
A catalog of appyter notebooks
NCI-GDC / gdc-docs
Forked from NCIP/gdc-docsOfficial repository for GDC User Guides in Markdown format
Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
This is a repository containing a single jupyter notebook that preprocesses TCGA data for use by gpmap tool from David McCandlish's lab
This notebook will access TCGA, preprocess those data, and perform common analyses.
Analysis examples based on the ISB-CGC hosted TCGA data, using Python and IPython Notebooks.
Jupyter Notebooks for RNA-seq TCGA/GTEx Cancer Study
Visualization and analysis of RNA-seq data from GTEx v8 in Jupyter Notebooks
a sample program to retrieve data from NCI's GDC data protal
A python package containing various tools for codon optimization and de-optimization.