Package: harmony 1.2.3

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✨
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NEWS

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

Peer review:

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).
  • 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.
  • pbmc.stim - 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.

On CRAN:

algorithmdata-integrationscrna-seq

13.97 score 527 stars 9 packages 4.8k scripts 9.4k downloads 6 mentions 5 exports 36 dependencies

Last updated 9 days agofrom:b36bab002c. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 11 2024
R-4.5-win-x86_64OKNov 11 2024
R-4.5-linux-x86_64OKNov 11 2024
R-4.4-win-x86_64OKNov 11 2024
R-4.4-mac-x86_64OKNov 11 2024
R-4.4-mac-aarch64OKNov 11 2024
R-4.3-win-x86_64OKNov 11 2024
R-4.3-mac-x86_64OKNov 11 2024
R-4.3-mac-aarch64OKNov 11 2024

Exports:%>%harmony_optionsHarmonyMatrixmoe_ridge_get_betasRunHarmony

Dependencies:clicolorspacecowplotdplyrfansifarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerRcppRcppArmadilloRcppProgressRhpcBLASctlrlangscalestibbletidyselectutf8vctrsviridisLitewithr

Detailed Walkthrough of Harmony Algorithm

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

Rendered fromdetailedWalkthrough.Rmdusingknitr::rmarkdownon Nov 11 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 Nov 11 2024.

Last update: 2024-11-11
Started: 2019-04-16

Using harmony in Seurat

Rendered fromSeurat.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2024-11-11
Started: 2023-09-20