harmony (version 1.2.3)

Fast, Sensitive, and Accurate Integration of Single Cell Data

Description

Implementation of the Harmony algorithm for single cell integration, described in Korsunsky et al . Package includes a standalone Harmony function and interfaces to external frameworks.

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Install

install.packages('harmony')

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9,880

Version

1.2.3

License

GPL-3

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Repository

https://github.com/immunogenomics/harmony

Maintainer

Ilya Korsunsky

Last Published

November 27th, 2024

Functions in harmony (1.2.3)

RunHarmony.SingleCellExperiment

Applies harmony on PCA cell embeddings of a SingleCellExperiment.

RunHarmony

Generic function that runs the harmony algorithm on single-cell genomics cell embeddings.

Gene expression data of stimulated PBMC from Kang et al. 2017. This contains a sample of 1000 cells from that condition and is used for the Seurat Vignette.

pbmc.ctrl

Gene expression data of control PBMC from Kang et al. 2017. This contains a sample of 1000 cells from that condition and is used for the Seurat Vignette.

cell_lines_small

Same as cell_lines but smaller (300 cells).

RunHarmony.Seurat

Applies harmony on a Seurat object cell embedding.

HarmonyMatrix

A proxy call to RunHarmony(). Deprecated.

RunHarmony.default

This is the primary harmony interface.

harmony_options

Set advanced parameters for RunHarmony

cell_lines

List of metadata table and scaled PCs matrix

harmony

Harmony: fast, accurate, and robust single cell integration.