Alternatives and similar repositories for ST-analysis

Users that are interested in ST-analysis are comparing it to the libraries listed below

• msraredon / NICHES
  Niche Interactions and Cellular Heterogeneity in Extracellular Signaling
  ☆56Updated 5 months ago
• aerickso / SpatialInferCNV
  Clone Calling from Visium Spatial Transcriptomics of Cancer samples
  ☆81Updated 2 years ago
• Teichlab / Genes2Genes
  Aligning gene expression trajectories of single-cell reference and query systems
  ☆76Updated 2 months ago
• KlugerLab / DAseq
  ☆41Updated 4 years ago
• jackbibby1 / SCPA
  R package for pathway analysis in scRNA-seq data
  ☆75Updated last year
• GfellerLab / SuperCell
  Coarse-graining of large single-cell RNA-seq data into metacells
  ☆90Updated 3 months ago
• rikenbit / scTensor
  R package for detection of cell-cell interaction using Non-negative Tensor Decomposition
  ☆34Updated 4 months ago
• FloWuenne / scFunctions
  Functions for single cell data analysis
  ☆32Updated 4 years ago
• phillipnicol / scDist
  Robust identification of perturbed cell types in single-cell RNA-seq data
  ☆34Updated 11 months ago
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆90Updated 2 months ago
• arc85 / singleseqgset
  Gene set enrichment analysis for single-cell RNAseq data
  ☆28Updated 2 years ago
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆89Updated 4 months ago
• arc85 / celltalker
  Inference of cell-cell communication from single-cell RNAseq data
  ☆48Updated 6 months ago
• jlaffy / infercna
  Infer Copy Number Alterations and Clonality in (Single-Cell) RNA-Seq Data
  ☆43Updated last year
• zijianni / SpotClean
  R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data
  ☆33Updated last year
• haniffalab / scRNA-seq_analysis
  Single cell RNA-seq analysis bundle
  ☆37Updated 6 years ago
• atakanekiz / CIPR-Package
  Cluster Identity Predictor (R package implementation)
  ☆20Updated 3 years ago
• JEFworks-Lab / CRAWDAD
  Cell-type Relationship Analysis Workflow Done Across Distances
  ☆38Updated 4 months ago
• califano-lab / single-cell-pipeline
  ☆50Updated 5 years ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆104Updated last year
• omnideconv / spacedeconv
  A unified interface to spatial transcriptomics deconvolution tools
  ☆42Updated 2 weeks ago
• Single-Cell-Genomics-Group-CNAG-CRG / Tumor-Immune-Cell-Atlas
  Code repository for the Tumor Immune Cell Atlas (TICA) project
  ☆64Updated 3 years ago
• ZJUFanLab / CellTalkDB
  A manually curated database of literature-supported ligand-receptor interactions in human and mouse
  ☆30Updated last year
• guokai8 / scGSVA
  scGSVA: Perform GSVA for single cell RNA seq
  ☆65Updated 11 months ago
• aet21 / SCENT
  Estimation of Single-Cell Potency with Single Cell Entropy
  ☆43Updated 2 years ago
• kaishumason / NicheDE
  NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data.
  ☆22Updated 4 months ago
• carmonalab / scGate
  marker-based purification of cell types from single-cell RNA-seq datasets
  ☆129Updated 3 months ago
• bdsc-tds / SPLIT
  Profile purification of single-cell spatial transcriptomics data
  ☆20Updated 2 months ago
• liziyie / scDVA
  An R shiny based tool used for single cell RNA-seq data visualization and analysis.
  ☆34Updated 4 years ago
• xmc811 / Scillus
  R Package for Single-Cell Dataset Processing and Visualization
  ☆64Updated 4 years ago