Alternatives and similar repositories for ST-analysis

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

• aerickso / SpatialInferCNV
  Clone Calling from Visium Spatial Transcriptomics of Cancer samples
  ☆74Updated 2 years ago
• jackbibby1 / SCPA
  R package for pathway analysis in scRNA-seq data
  ☆75Updated 11 months ago
• msraredon / NICHES
  Niche Interactions and Cellular Heterogeneity in Extracellular Signaling
  ☆55Updated 3 months ago
• liziyie / scDVA
  An R shiny based tool used for single cell RNA-seq data visualization and analysis.
  ☆33Updated 4 years ago
• GfellerLab / SuperCell
  Coarse-graining of large single-cell RNA-seq data into metacells
  ☆87Updated last month
• califano-lab / single-cell-pipeline
  ☆50Updated 5 years ago
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆86Updated 2 months ago
• ccruizm / GBmap
  Code used to create the core and extended GBmap, including downstream analyses (cell-cell interactions, spatial transcriptomics deconvolu…
  ☆58Updated 2 years ago
• KlugerLab / DAseq
  ☆41Updated 4 years ago
• tiroshlab / 3ca
  Code for reproducing the analysis in Gavish et al. "The transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors".
  ☆120Updated 11 months ago
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆85Updated 2 months ago
• FloWuenne / scFunctions
  Functions for single cell data analysis
  ☆32Updated 4 years ago
• arc85 / celltalker
  Inference of cell-cell communication from single-cell RNAseq data
  ☆48Updated 3 months ago
• jlaffy / scalop
  Single Cell Analysis Operations
  ☆13Updated 4 months ago
• guokai8 / scGSVA
  scGSVA: Perform GSVA for single cell RNA seq
  ☆64Updated 8 months ago
• ZJUFanLab / CellTalkDB
  A manually curated database of literature-supported ligand-receptor interactions in human and mouse
  ☆31Updated last year
• jlaffy / infercna
  Infer Copy Number Alterations and Clonality in (Single-Cell) RNA-Seq Data
  ☆42Updated last year
• yanailab / PanCancer
  Data available at: https://www.dropbox.com/sh/jh4s57kgbb0rnxe/AABoMK466cGc1OKsOuFN10wca?dl=0 and https://nyulangone-my.sharepoint.com//g/…
  ☆31Updated 2 years ago
• RausellLab / CelliD
  Gene signature extraction and cell-identity recognition at individual cell level from single-cell RNA-seq.
  ☆95Updated last year
• Coolgenome / iTALK
  ☆61Updated 6 years 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
• Teichlab / Genes2Genes
  Aligning gene expression trajectories of single-cell reference and query systems
  ☆73Updated 9 months ago
• Teichlab / Pan_fetal_immune
  Collection of scripts for analysis of pan fetal immune atlas
  ☆27Updated 2 years ago
• atakanekiz / CIPR-Package
  Cluster Identity Predictor (R package implementation)
  ☆20Updated 3 years ago
• vertesy / Seurat.utils
  Various utility functions for Seurat single-cell analysis
  ☆52Updated last week
• powellgenomicslab / Nebulosa
  R package to visualize gene expression data based on weighted kernel density estimation
  ☆103Updated last year
• zijianni / SpotClean
  R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data
  ☆32Updated last year
• ShellyCoder / cellcall
  inferring cell-cell communication from scRNA-seq of ligand-receptor
  ☆83Updated last year
• Japrin / STARTRAC
  STARTRAC(Single T-cell Analysis by Rna-seq and Tcr TRACking)
  ☆107Updated 3 months ago
• califano-lab / PISCES
  R package for Protein activity analysis of single-cell RNAseq.
  ☆83Updated 2 years ago