MargoKapustina / XeniumSpatialAnalysis
R-based Xenium Spatial Analysis Toolkit to assess gene expression gradients
☆14Updated 4 months ago
Alternatives and similar repositories for XeniumSpatialAnalysis:
Users that are interested in XeniumSpatialAnalysis are comparing it to the libraries listed below
- Cluster Identity Predictor (R package implementation)☆20Updated 3 years ago
- ☆21Updated last month
- Spatial transcriptomics analyses and decoding in R☆18Updated last month
- Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics☆33Updated 2 weeks ago
- This repository contains scripts to identify healthy and malignant cells from scRNAseq with CloneTracer and process data from Optimized 1…☆25Updated 5 months ago
- Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes☆43Updated 3 years ago
- code for data processing and visualisation associated with the stromal subclasses manuscript☆11Updated 4 years ago
- Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity☆25Updated 8 months ago
- Scripts and notebooks to reproduce all analysis from Massoni-Badosa et al. (2022)☆28Updated 2 months ago
- Repository for "Effective methods for bulk RNA-seq deconvolution using scRNA-seq and snRNA-seq derived transcriptomes"☆15Updated last year
- An R package for handling and analysing imaging mass cytometry data☆24Updated 4 months ago
- ☆33Updated 11 months ago
- An R implementation of the Gene Frequency - Inverse Cell Frequency method for single cell data normalization☆18Updated last year
- Pipeline for designing custom probes against human genes☆16Updated 4 months ago
- Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression☆26Updated 3 months ago
- Stitch multiple Visium slides together☆15Updated last year
- ☆9Updated 8 months ago
- R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data☆31Updated 9 months ago
- A manually curated database of literature-supported ligand-receptor interactions in human and mouse☆29Updated 8 months ago
- ☆47Updated 2 years ago
- General notes and resources on how to analyze Spatial Transcriptomics data☆12Updated last year
- Inference of Minimal Event Distance Aneuploidy Lineage Tree based on single cell copy number profile☆19Updated last year
- NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data.☆17Updated 5 months ago
- cell type deconvolution for multi-condition bulk RNA-seq data☆23Updated 3 years ago
- ☆13Updated last year
- A unified interface to spatial transcriptomics deconvolution tools☆40Updated 3 weeks ago
- Identify genes with spatial expression trends in single-cell gene expression data☆50Updated 7 years ago
- The SpatialDecon library implements the SpatialDecon algorithm for mixed cell deconvolution in spatial gene expression datasets. (This al…☆37Updated 3 months ago
- This repository contains code for the evaluation of epithelial-to-mesenchymal transition states in cancer.☆12Updated 2 years ago
- sharing interactive single cell gene expression visualizations from Seurat☆10Updated last year