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Clone Calling from Visium Spatial Transcriptomics of Cancer samples
Spot pseudo-Imager on top of histology
Repository for ENACT pipeline for end-to-end analysis of Visium HD data
DEMINING: a stepwise computational framework to directly detect expressed DNA and RNA mutations in RNA deep sequencing data (DEMINING).
Repository for all R scripts used for the bioinformatic analyses of the mouse and human 10x Genomics Visium spatially resolved transcriptomics data presented in our associated manuscript.
The current study provides a comprehensive insights into the PDAC metastatic biology.
Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
Interfaces for HDF5-based Single Cell File Formats
Public repo for STEP: Spatial Transcriptomics Embedding Procedure
Quantifying metabolism activity at the single-cell resolution
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
Deep Transfer Learning of Drug Sensitivity by Integrating Bulk and Single-cell RNA-seq data