Alternatives and similar repositories for spatialGE

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

• quadbio / organoid_regulomes
  Reproducibility code for the manuscript: 'Inferring and perturbing cell fate regulomes in human cerebral organoids
  ☆28Updated last year
• hsmaan / Iniquitate
  Analysis of imbalanced data and its impacts in a scRNA-seq integration setting
  ☆30Updated 2 months ago
• raphael-group / CalicoST
  Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
  ☆35Updated 3 weeks ago
• saezlab / MOFAcellulaR
  R package to infer multicellular programs from single-cell data using multi-omics factor analysis (MOFA)
  ☆10Updated last year
• davidliwei / PS
  Perturbation-response Score (PS) analysis is a method to quantify diverse perturbation responses and discover novel biological insights i…
  ☆14Updated last year
• elo073 / 5loclung
  Custom codes accompanying single cell spatial transcriptomic study on the healthy human lung
  ☆12Updated last year
• GreenleafLab / brainchromatin
  Code used to analyze single cell RNA and ATAC sequencing in developing human brain
  ☆33Updated 3 years ago
• pachterlab / FGP_2024
  ☆14Updated 3 months ago
• wanglab-broad / CAST
  CAST package
  ☆38Updated 7 months ago
• limix / CellRegMap
  CellRegMap: A statistical framework for mapping context-specific regulatory variants using scRNA-seq
  ☆22Updated 9 months ago
• MarioniLab / StabMap
  Mosaic single cell data integration using non-overlapping features
  ☆37Updated 2 years ago
• AllenInstitute / scrattch.bigcat
  iterative clustering pipeline of big single cell datasets.
  ☆31Updated 3 weeks ago
• KChen-lab / bindSC
  Bi-order integration (in silico multi-omics data) of single cell RNA sequencing, single cell ATAC sequencing, spacial transcriptomics and…
  ☆35Updated last year
• CamaraLab / ConDecon
  R package: ConDecon is a clustering-independent deconvolution method for estimating cell abundances in bulk tissues using single-cell RNA…
  ☆12Updated 7 months ago
• zhang-bin-98 / A-spatial-transcriptome-landscape-of-mouse-aging
  ☆13Updated 6 months ago
• jbergenstrahle / STUtility
  ☆52Updated 2 years ago
• CamaraLab / STvEA
  Spatially-resolved Transcriptomics via Epitope Anchoring
  ☆19Updated last year
• kaishumason / NicheDE
  NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data.
  ☆18Updated 7 months ago
• dpeerlab / pdac-progression
  ☆10Updated 2 years ago
• HectorRDB / condiments
  Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
  ☆28Updated 5 months ago
• wanglabtongji / CCI
  Evaluation of cell-cell interaction methods by integrating single-cell RNA sequencing data with spatial information
  ☆21Updated 2 years ago
• alexQiSong / scSTEM
  Single cell STEM (scSTEM) is a shiny app based R package for visualizing and clustering genes in pseudotime ordered single cell RNA-seq d…
  ☆18Updated 2 years ago
• TrigosTeam / SPIAT
  ☆23Updated 2 months ago
• theislab / cross_system_integration
  ☆13Updated last month
• hkim240 / CellNeighborEX
  CellNeighborEX: Deciphering Neighbor-Dependent Gene Expression from Spatial Transcriptomics Data
  ☆14Updated 10 months ago
• WWXkenmo / ICAnet
  Independent Component Analysis decipher functional modules for better cell clustering and annotation
  ☆15Updated 3 years ago
• miccec / GBMstates
  Scripts from the GBM cellular states paper
  ☆18Updated 4 years ago
• pinellolab / STREAM2
  STREAM2: Fast, scalable, and interactive trajectory analysis of single-cell omics data
  ☆10Updated last year
• theMILOlab / SPATA
  SPATA Package for spatial gene expression analysis
  ☆23Updated 3 years ago
• JEFworks-Lab / CRAWDAD
  Cell-type Relationship Analysis Workflow Done Across Distances
  ☆31Updated 3 months ago