Alternatives and similar repositories for CISI

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

• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆30Updated last year
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆57Updated 4 months ago
• Nanostring-Biostats / SpatialOmicsOverlay
  Tools for analyzing data on the image from NanoString GeoMx Digital Spatial Profiler (DSP).
  ☆23Updated last month
• ZhuangLab / MERlin
  MERFISH decoding software
  ☆26Updated 3 months ago
• suinleelab / contrastiveVI
  ☆57Updated last year
• PMBio / SpatialDE
  Test genes for Spatial Variation
  ☆15Updated 11 months ago
• FridleyLab / spatialGE
  Methods for visualization and analysis of spatially-resolved gene expression
  ☆21Updated 3 months ago
• willtownes / spatial-factorization-py
  Probabilistic factor models for spatially correlated data. Includes nonnegative and real-valued versions.
  ☆16Updated 11 months ago
• AllenInstitute / mfishtools
  Building Gene Sets and Mapping mFISH Data
  ☆16Updated 3 months ago
• mbernste / SpatialCorr
  SpatialCorr: Identify gene sets with spatially varying correlation
  ☆17Updated last year
• damienArnol / svca
  ☆13Updated 6 years ago
• KenLauLab / DR-structure-preservation
  A quantitative framework for evaluating data structure preservation by dimensionality reduction techniques
  ☆16Updated 4 years ago
• BodenmillerGroup / SCPathology_publication
  The Single-Cell Pathology Landscape of Breast Cancer
  ☆27Updated 5 years ago
• willtownes / nsf-paper
  Nonnegative spatial factorization for multivariate count data
  ☆61Updated 2 years ago
• almaan / eggplant
  ☆22Updated 3 years ago
• bm2-lab / SpaDo
  Multi-slice Spatial Transcriptome Domain Analysis.
  ☆12Updated 11 months ago
• ElementoLab / utag
  ☆39Updated last year
• wanglab-broad / CAST
  CAST package
  ☆40Updated last year
• PYangLab / Matilda
  Matilda is a multi-task framework for learning from single-cell multimodal omics data. Matilda leverages the information from the multi-m…
  ☆22Updated 5 months ago
• QihuangZhang / CeLEry
  CeLEry: cell location recovery in single-cell RNA sequencing
  ☆35Updated 9 months ago
• Mr-Milk / SpatialTis
  Spatial analysis toolkit for single cell multiplexed tissue data
  ☆30Updated last year
• yozhikoff / segmentation
  End-to-end pipeline for segmenting cell nuclei on histology slides
  ☆16Updated 3 years ago
• HiDiHlabs / SpatialLeiden
  Implementation of multiplex Leiden for analysis of spatial omics data
  ☆13Updated last month
• huBioinfo / CytoCommunity
  A spatial omics data analysis tool that enables both unsupervised and supervised discovery of complex tissue cellular neighborhoods from …
  ☆26Updated 7 months ago
• CaiGroup / seqFISH-PLUS
  ☆52Updated 4 years ago
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆25Updated last year
• seqscope / ficture
  ☆39Updated 3 weeks ago
• shuxiaoc / mario-py
  MARIO: single-cell proteomic data matching and integration using both shared and distinct features
  ☆22Updated 2 years ago
• sfortma2 / scranPY
  A python implementation of scran computeSumFactors: normalization by deconvolution for single-cell RNA-sequencing
  ☆35Updated 2 years ago
• feiyoung / PRECAST
  an efficient data integration method for multiple spatial transcriptomics data with non- cluster-relevant effects such as the complex batc…
  ☆12Updated last month