From: Community-wide hackathons to identify central themes in single-cell multi-omics
Type | Name | Description |
---|---|---|
Matlab package | CytoMAP: A Spatial Analysis Toolbox Reveals Features of Myeloid Cell Organization in Lymphoid Tissues | |
Matlab package | histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data | |
Python library | General framework for deep learning | |
Python & R | General framework for deep learning | |
Python package | SpaCell: integrating tissue morphology and spatial gene expression to predict disease cells | |
Python package | Python package for single-cell analysis | |
R data class | unify multiple experiments | |
R data class | SpatialExperiment: a collection of S4 classes for Spatial Data | |
R package | Spatial transcriptomics | |
R package | cytomapper: Visualization of highly multiplexed imaging cytometry data in R | |
R package | Spaniel: analysis and interactive sharing of Spatial Transcriptomics data | |
R package | R toolkit for single-cell genomics | |
R package | Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex | |
R package | Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments | |
R package | scCoGAPS learns biologically meaningful latent spaces from sparse scRNA-Seq data | |
R package | ProjectR is a transfer learning framework to rapidly explore latent spaces across independent datasets | |
R package | Serves multiple datasets obtained from GEO and other sources and represents them as MultiAssayExperiment objects | |
R scripts | Scripts for SpatialExperiment usage | |
Self-contained GUI | ST viewer: a tool for analysis and visualization of spatial transcriptomics datasets | |
Shiny app | A comparison of single-cell trajectory inference methods: towards more accurate and robust tools | |
R package | R toolkit for multivariate analysis of multi-modal data | |
R package | R package for dimension reduction and integration of single-cell data, using correspondence analysis | |
Python package | 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 | Interactive big multi-dimensional 3D image viewer | |
Software | Multiplex whole slide image analysis | |
Python package | Multiplex whole slide image analysis | |
Python package | Multiplex whole slide image analysis | |
Software | Multiplex whole slide image analysis, not available yet | |
Software, Python based | Image analysis | |
Python library | Spatial single-cell analysis |