CellTrek

Cell charting toolkit

A toolkit for mapping single cells to spatial coordinates in tissue sections based on scRNA-seq and ST data

GitHub

108 stars
3 watching
19 forks
Language: R
last commit: over 2 years ago

Related projects:

Repository Description Stars
navinlabcode/copykat A tool for inferring genomic copy number and subclonal structure from single cell RNA sequencing data. 209
cellgeni/scrna.seq.course An educational resource teaching computational analysis of single-cell RNA-seq data using R and Bioconductor tools 123
tanaylab/metacell An R package that facilitates analysis of single-cell RNA-seq data by identifying homogeneous groups of cells. 108
zjufanlab/spatalk An R package that infers cell-cell communication and ligand-receptor-target networks from spatially resolved transcriptomic data 62
rajewsky-lab/novosparc Software tool to predict spatial locations of single cells in tissue using single-cell RNA sequencing data 126
zjufanlab/sccatch Automated tool for annotating cell types from single-cell RNA sequencing data based on marker genes 218
batzogloulabsu/simlr An implementation of a machine learning method for analyzing single-cell RNA-seq data, providing tools for dimension reduction, clustering, and visualization. 109
pfprzytycki/cellwalkr An R package for integrating and visualizing single-cell and bulk data to identify cell type-specific regulatory regions. 10
royerlab/ultrack A software framework for robust cell tracking in 2D, 3D, and multichannel images with uncertain segmentation 94
martaint/intercellar An interactive R/Shiny app for analyzing cell-cell communication from single-cell transcriptomics data 9
yulab-smu/ggsc A package for visualizing single cell and spatial transcriptomics data using R 43
ncborcherding/screpertoire A toolkit for analyzing single-cell immune data from various formats using machine learning and bioinformatics techniques. 310
nbisweden/excelerate-scrnaseq An open-source R package providing tools and methods for analyzing single cell RNA-seq data 216
dtm2451/dittoseq A suite of functions for analyzing and visualizing RNA sequencing data 190
angelolab/ark-analysis A toolset for analyzing multiplexed imaging data by applying various machine learning and image processing techniques to segment cells, cluster pixels, and perform spatial analysis. 76