Stars
Toolbox of the Human Neural Organoid Cell Atlas
Interpretable Vision-Language Survival Analysis with Ordinal Inductive Bias for Computational Pathology (ICLR 2025)
CytoTRACE 2 is an interpretable AI method for predicting cellular potency and absolute developmental potential from scRNA-seq data.
R package providing tools for enrichment calculations, access to multiple reference gene sets such as GO, KEGG, Reactome as well as more specialized collections of gene sets collected from publishe…
marker-based purification of cell types from single-cell RNA-seq datasets
Code associated with the data analysis for Miyoshi & Morabito 2024
Comprehensive list of color palettes available in R ❤️🧡💛💚💙💜
PolyFun (POLYgenic FUNctionally-informed fine-mapping)
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
scRNAseq analysis notes from Ming Tang
Arc Virtual Cell Atlas
main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org
A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to represent new studies without additional training.
List of software packages for multi-omics analysis
List of software packages for multi-trait / multiple-trait / multivariate / high-dimensional GWAS
SCISSORS builds upon the Louvain graph-based clustering in Seurat by optimizing parameter selection when reclustering cell groups, with an eye towards identifying rare cell types.
AI-based differential diagnosis of dementia etiologies on multimodal data
A package to help convert different single-cell data formats to each other
Reproducibility repository for the Human Neural Organoid Atlas publication
An LC-MS/MS glycan and glycopeptide search engine
This project provides an easy R function for translating R Markdown (.rmd) files to Jupyter Notebook (.ipynb) files.
Molecular QTL analysis protocol developed by ADSP Functional Genomics Consortium