Package: harmony 1.2.3
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:
harmony_1.2.3.tar.gz
harmony_1.2.3.tar.gz(r-4.5-noble)harmony_1.2.3.tar.gz(r-4.4-noble)
harmony_1.2.3.tgz(r-4.4-emscripten)harmony_1.2.3.tgz(r-4.3-emscripten)
harmony.pdf |harmony.html✨
harmony/json (API)
NEWS
# Install 'harmony' in R: |
install.packages('harmony', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/immunogenomics/harmony/issues
- 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.
Last updated 10 days agofrom:34bb5ff380. Checks:OK: 2. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 28 2024 |
R-4.5-linux-x86_64 | OK | Nov 28 2024 |
Exports:%>%harmony_optionsHarmonyMatrixmoe_ridge_get_betasRunHarmony
Dependencies:clicolorspacecowplotdplyrfansifarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerRcppRcppArmadilloRcppProgressRhpcBLASctlrlangscalestibbletidyselectutf8vctrsviridisLitewithr
Detailed Walkthrough of Harmony Algorithm
Rendered fromdetailedWalkthrough.Rmd
usingknitr::rmarkdown
on Nov 28 2024.Last update: 2023-11-30
Started: 2023-09-20
Quick start to Harmony
Rendered fromquickstart.Rmd
usingknitr::rmarkdown
on Nov 28 2024.Last update: 2024-11-28
Started: 2021-06-02
Using harmony in Seurat
Rendered fromSeurat.Rmd
usingknitr::rmarkdown
on Nov 28 2024.Last update: 2024-11-28
Started: 2023-09-20