R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

This repository contains the code used to generate figures and perform analysis for the manuscript titled "Transcriptomic and Spatial Proteomic Profiling Reveals the Cellular Composition and Spatia…

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

SPLICE-q -- A Python tool for genome-wide SPLIcing Efficiency quantification from RNA-seq data.

IMC_Denoise: a software package to enhance Imaging Mass Cytometry - Nature Communications

Run current & prior versions of R using docker. rocker/r-ver, rocker/rstudio, rocker/shiny, rocker/tidyverse, and so on.

Inferring CNV from Single-Cell RNA-Seq

R package for modeling single cell UMI expression data using regularized negative binomial regression

Histology Topography Cytometry Analysis Toolbox

HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data

R toolkit for single cell genomics