Stars
R package for integrating and analyzing multiple single-cell datasets
Harmonization of multi-site imaging data with ComBat
R package for semi-supervised single-cell data integration
characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities
Statistical approach for removing unwanted variation from multiple single-cell datasets
Niche Interactions and Cellular Heterogeneity in Extracellular Signaling
Code for major analyses in "Integrative spatial analysis reveals a multi-layered organization of glioblastoma" paper
Correcting Covariance Batch Effects (CovBat): Harmonization of mean and covariance for multi-site data
nnSVG: scalable method to identify spatially variable genes (SVGs) in spatially-resolved transcriptomics data
Methods for visualization and analysis of spatially-resolved gene expression
This repository contains the code for all figures in the paper "General Pitfalls of Model-agnostic Interpretation Methods for Machine Learning Models"
AC-PCA: simultaneously performs dimension reduction and adjustment for confounding variation
The R package varycoef implements Gaussian processes spatially varying coefficient models.
Code for reproducing the main figures in https://arxiv.org/abs/2106.00170.
A metric for relative distance in Poisson sampling problems
Semiparametric Spatial Filtering with Eigenvectors in (Generalized) Linear Models
This repository implements the Integrated R-squared Dependence (IRDC) coefficient and Feature Ordering by Integrated R-squared Dependence (FORD), which are used for variable selection.
A package for discovering and correcting for batch effect using an approach in Nyamundanda et al (2017).
Crescendo for single-gene correction in single-cell RNA-sequencing data
MonteCarloCooperativeGames is an R package for simulating large cooperative games and approximating the Shapley value and related point-valued solution concepts.