Package: harmony 1.2.0

Ilya Korsunsky

harmony: Fast, Sensitive, and Accurate Integration of Single Cell Data

Implementation of the Harmony algorithm for single cell integration, described in Korsunsky et al <doi:10.1038/s41592-019-0619-0>. Package includes a standalone Harmony function and interfaces to external frameworks.

Authors:Ilya Korsunsky [cre, aut], Martin Hemberg [aut], Nikolaos Patikas [aut, ctb], Hongcheng Yao [aut, ctb], Nghia Millard [aut], Jean Fan [aut, ctb], Kamil Slowikowski [aut, ctb], Miles Smith [ctb], Soumya Raychaudhuri [aut]

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harmony.pdf |harmony.html✨
harmony/json (API)
NEWS

# Install 'harmony' in R:

install.packages('harmony', repos = c('https://immunogenomics.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/immunogenomics/harmony/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

cell_lines - List of metadata table and scaled PCs matrix
cell_lines_small - Same as cell_lines but smaller (300 cells).

On CRAN:

algorithm data-integration scrna-seq

5 exports 510 stars 7.61 score 36 dependencies 7 dependents 6 mentions 4.0k scripts 5.9k downloads

Last updated 10 months agofrom:f054b030b5. Checks:OK: 1 WARNING: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Aug 28 2024
R-4.5-win-x86_64	WARNING	Aug 28 2024
R-4.5-linux-x86_64	WARNING	Aug 28 2024
R-4.4-win-x86_64	WARNING	Aug 28 2024
R-4.4-mac-x86_64	WARNING	Aug 28 2024
R-4.4-mac-aarch64	WARNING	Aug 28 2024
R-4.3-win-x86_64	WARNING	Aug 28 2024
R-4.3-mac-x86_64	WARNING	Aug 28 2024
R-4.3-mac-aarch64	WARNING	Aug 28 2024

Exports:%>%harmony_options HarmonyMatrix moe_ridge_get_betas RunHarmony

Dependencies:cli colorspace cowplot dplyr fansi farver generics ggplot2 glue gtable isoband labeling lattice lifecycle magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig R6 RColorBrewer Rcpp RcppArmadillo RcppProgress RhpcBLASctl rlang scales tibble tidyselect utf8 vctrs viridisLite withr

Detailed Walkthrough of Harmony Algorithm

Korsunsky et al.: Fast, sensitive, and accurate integration of single cell data with Harmony

Rendered fromdetailedWalkthrough.Rmdusingknitr::rmarkdownon Aug 28 2024.

Last update: 2023-11-10
Started: 2023-09-20

Quick start to Harmony

Korsunsky et al.: Fast, sensitive, and accurate integration of single cell data with Harmony

Rendered fromquickstart.Rmdusingknitr::rmarkdownon Aug 28 2024.

Last update: 2023-09-29
Started: 2019-04-16

Using harmony in Seurat

Rendered fromSeurat.Rmdusingknitr::rmarkdownon Aug 28 2024.

Last update: 2023-09-29
Started: 2023-09-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
List of metadata table and scaled PCs matrix	cell_lines
Same as cell_lines but smaller (300 cells).	cell_lines_small
Harmony: fast, accurate, and robust single cell integration.	harmony
Set advanced options for RunHarmony	harmony_options
Get beta Utility	moe_ridge_get_betas
Generic function that runs the harmony algorithm on single-cell genomics cell embeddings.	RunHarmony
This is the primary harmony interface.	RunHarmony.default
Applies harmony on a Seurat object cell embedding.	RunHarmony.Seurat
Applies harmony on PCA cell embeddings of a SingleCellExperiment.	RunHarmony.SingleCellExperiment