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Table 1 List of software for multi-modal single-cell analysis

From: Community-wide hackathons to identify central themes in single-cell multi-omics

Type Name Description
Matlab package CytoMAP CytoMAP: A Spatial Analysis Toolbox Reveals Features of Myeloid Cell Organization in Lymphoid Tissues
Matlab package histoCAT histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data
Python library PyTorch General framework for deep learning
Python & R TensorFlow General framework for deep learning
Python package SpaCell SpaCell: integrating tissue morphology and spatial gene expression to predict disease cells
Python package Scanpy Python package for single-cell analysis
R data class MultiAssayExperiment unify multiple experiments
R data class SpatialExperiment SpatialExperiment: a collection of S4 classes for Spatial Data
R package Giotto Spatial transcriptomics
R package cytomapper cytomapper: Visualization of highly multiplexed imaging cytometry data in R
R package Spaniel Spaniel: analysis and interactive sharing of Spatial Transcriptomics data
R package Seurat R toolkit for single-cell genomics
R package SpatialLIBD Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
R package Cardinal Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments
R package CoGAPS scCoGAPS learns biologically meaningful latent spaces from sparse scRNA-Seq data
R package projectR ProjectR is a transfer learning framework to rapidly explore latent spaces across independent datasets
R package SingleCellMultiModal Serves multiple datasets obtained from GEO and other sources and represents them as MultiAssayExperiment objects
R scripts SpatialAnalysis Scripts for SpatialExperiment usage
Self-contained GUI ST viewer ST viewer: a tool for analysis and visualization of spatial transcriptomics datasets
Shiny app Dynverse A comparison of single-cell trajectory inference methods: towards more accurate and robust tools
R package mixOmics R toolkit for multivariate analysis of multi-modal data
R package Corral R package for dimension reduction and integration of single-cell data, using correspondence analysis
Python package totalVI A variational autoencoder (deep learning model) to integrate RNA and protein data from CITE-seq experiments
Python web application ImJoy Deep learning web interface
Python package napari Interactive big multi-dimensional 3D image viewer
Software QuPath Multiplex whole slide image analysis
Python package Cytokit Multiplex whole slide image analysis
Python package cmIF Multiplex whole slide image analysis
Software Facetto Multiplex whole slide image analysis, not available yet
Software, Python based CellProfiler Image analysis
Python library Squidpy Spatial single-cell analysis