Analysis Tools Registry

Methods Packages

Methods packages listed below are tools for performing analyses involving computational biology approaches for analyzing single cell data. Method software is pre-installed in container images. Registry methods can be called programmatically for easy integration into portals. These methods provide domain-specific ways to analyze biological data produced by Human Cell Atlas.

These solutions are built by third parties, and fostered by the HCA DCP.

Are you developing a package that can consume HCA data? Please submit it for inclusion in the registry.

Markov Affinity-based Graph Imputation of Cells (MAGIC)

David van Dijk, Kevin Moon, Scott Gigante, Daniel Dager, Guy Wolf, Smita Krishnaswamy

Markov Affinity-based Graph Imputation of Cells (MAGIC) is an algorithm for denoising and imputation of single cells applied to single-cell RNA sequencing data

Potential of Heat-diffusion for Affinity-based Transition Embedding (PHATE)

Kevin Moon, David van Dijk, Scott Gigante, Smita Krishnaswamy

PHATE is a tool for visualizing high dimensional single-cell data with natural progressions or trajectories.

Single-cell consensus clustering (SC3)

Martin Hemberg (SC3), Gene Expression Team (sc3-scripts)

SC3 is an unsupervised clustering method for scRNA-seq data.


Kelly Street, Davide Risso, Diya Das, Sandrine Dudoit, Koen Van den Berge, and Robrecht Cannoodt

Slingshot provides functions for inferring continuous, branching lineage structures in low-dimensional data.

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data

Huidong Chen, Luca Pinello

STREAM is an interactive computational pipeline for reconstructing complex cellular developmental trajectories from sc-qPCR, scRNA-seq or scATAC-seq data.

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