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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