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Framework

Summary Table

NAME CATEGORY CITATION YEAR
Scanpy Comprehensive NA NA
Seurat Comprehensive NA NA
OmicsTweezer Single_Cell NA NA
Giotto Spatial NA NA
Squidpy Spatial NA NA

Comprehensive

Scanpy

Seurat

  • NAME : Seurat

Single_Cell

OmicsTweezer

  • NAME : OmicsTweezer
  • SHORT NAME : OmicsTweezer
  • FULL NAME : OmicsTweezer: A distribution-independent cell deconvolution model for multi-omics Data
  • DESCRIPTION : Unified framework integrating optimal transport with deep learning to deconvolve bulk RNA-seq, proteomics, and spatial transcriptomics data while mitigating batch effects
  • URL : https://github.com/Fry2024/OmicsTweezer
  • KEYWORDS : cell deconvolution, optimal transport, deep learning, spatial transcriptomics, proteomics
  • USE : Estimates cell type proportions from bulk omics data by aligning simulated and real data distributions
  • PREPRINT_DOI : 10.1016/j.xgen.2025.100950
  • SERVER : Cell Genomics

Spatial

Giotto

  • NAME : Giotto
  • DESCRIPTION : The Giotto package consists of two modules, Giotto Analyzer and Viewer (see www.spatialgiotto.com), which provide tools to process, analyze and visualize single-cell spatial expression data.
  • URL : https://rubd.github.io/Giotto_site/
  • PUBMED_LINK : 33685491

Squidpy