Alternatives and similar repositories for CellTrek

Users that are interested in CellTrek are comparing it to the libraries listed below

• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆129Updated 4 months ago
• Teichlab / cellhint
  A tool for semi-automatic cell type harmonization and integration
  ☆107Updated 2 months ago
• carmonalab / GeneNMF
  Methods to discover gene programs on single-cell data
  ☆124Updated last week
• tiroshlab / 3ca
  Code for reproducing the analysis in Gavish et al. "The transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors".
  ☆116Updated 9 months ago
• YMa-lab / CARD
  ☆119Updated last year
• Sijin-ZhangLab / PanMyeloid
  ☆104Updated 4 years ago
• aerickso / SpatialInferCNV
  Clone Calling from Visium Spatial Transcriptomics of Cancer samples
  ☆71Updated 2 years ago
• ShellyCoder / cellcall
  inferring cell-cell communication from scRNA-seq of ligand-receptor
  ☆82Updated last year
• prabhakarlab / Banksy
  BANKSY: spatial clustering
  ☆112Updated last week
• saeyslab / multinichenetr
  MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…
  ☆147Updated 5 months ago
• 10XGenomics / HumanColonCancer_VisiumHD
  Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using h…
  ☆80Updated last week
• chuiqin / irGSEA
  The integration of single cell rank-based gene set enrichment analysis
  ☆124Updated 10 months ago
• zhengrongbin / MEBOCOST
  A python-based package and software to predict metabolite mediated cell-cell communications by single-cell RNA-seq data
  ☆76Updated 7 months ago
• saezlab / visium_heart
  Spatial transcriptomics of heart tissue
  ☆87Updated last year
• Japrin / STARTRAC
  STARTRAC(Single T-cell Analysis by Rna-seq and Tcr TRACking)
  ☆105Updated last month
• igrabski / sc-SHC
  Significance analysis for clustering single-cell RNA-sequencing data
  ☆116Updated 9 months ago
• matanhofree / crc-immune-hubs
  Principal analysis code used in for analysis of single cell RNAseq of primary untreated colon cancer. As described in: "Spatially organiz…
  ☆39Updated 3 years ago
• Yelab2020 / Cottrazm
  Construct Tumor Transition Zone Microenvironment
  ☆44Updated 7 months ago
• almaan / stereoscope
  Spatial mapping of cell types by integration of transcriptomics data
  ☆93Updated 2 years ago
• jfnavarro / st_pipeline
  ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method …
  ☆84Updated 3 months ago
• immunogenomics / LISI
  Methods to compute Local Inverse Simpson's Index (LISI)
  ☆62Updated 3 years ago
• swaruplab / Single-nuclei-epigenomic-and-transcriptomic-landscape-in-Alzheimer-disease
  Single-nuclei RNA-seq and ATAC-seq in Alzheimer's disease
  ☆93Updated 3 years ago
• LungCellAtlas / HLCA_reproducibility
  This repository contains all code used for the Human Lung Cell Atlas project.
  ☆49Updated last year
• Sanofi-Public / enact-pipeline
  Repository for ENACT pipeline for end-to-end analysis of Visium HD data
  ☆51Updated last week
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆102Updated 9 months ago
• Teichlab / bin2cell
  Join subcellular Visium HD bins into cells
  ☆111Updated last month
• quadbio / scMultiome_analysis_vignette
  Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis
  ☆58Updated last year
• immunogenomics / symphony
  Efficient and precise single-cell reference atlas mapping with Symphony
  ☆105Updated 2 years ago
• wu-yc / scMetabolism
  Quantifying metabolism activity at the single-cell resolution
  ☆136Updated 10 months ago
• PaulingLiu / ROGUE
  Assessing the purity of single cell population
  ☆129Updated 3 years ago