Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity

Source code for MIA from Moncada et al Nature Biotechnology (2020)

Single-Cell Clustering Assessment Framework

Senescent Cell Identification

An R package to plot maps of clone distributions in somatic evolution

Single-Sample Predictors for Breast Cancer (sspbc) include functions and models to assign classes to breast cancer samples using gene expression data.

Single Cell Oriented Reconstruction of PANDA-based Individually Optimized Networks

Code for ST_IGI package

Message Passing Neural Networks for Molecule Property Prediction

PyTorch implementation of Owkin's CHOWDER Method

Synthetic histology using GANs, for deep learning model explainability and trainee education.

Bayesian Inference of Slide-level Confidence via Uncertainty Index Thresholding

Compute and display Kaplan-Meier Curves with ggplot2

🧬 Gene analysis toolkit based on R

An R package to calculate Dynamical Network Biomarkers (DNB).

Rphenograph: R implementation of the PhenoGraph algorithm

Subpopulation detection in high-dimensional single-cell data

removes batch effects, good for small sample sizes, mean-centric

Pseudobulk analysis for scRNAseq with bootstrapping

R wrappers to connect Python dimensional reduction tools and single cell data objects (Seurat, SingleCellExperiment, etc...)

Unsupervised Inference of Developmental Directions for Single Cells

Packaged implementation of consensus nonnegative matrix factorization (cNMF; Kotliar, et al. 2019) for single-cell data analysis

An R package to infer cell-cell interactions and clinical values in tumor immune microenvironment through gene pairs.

Pipeline that runs two-sample Mendelian randomization on molecular QTLs and GWAS loci and tests for horizontal pleiotropy.

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.