References

Asc-Seurat is built on the work of many other people and relies on a diversity of R packages. These packages, in turn, have many dependencies. Here we list all packages that Asc-Seurat directly calls.

Analytical core

• Seurat

  • web page: https://satijalab.org/seurat/

  • Publications:

    • Satija, R. et al. (2015) Spatial reconstruction of single-cell gene expression data. Nat. Biotechnol., 33, 495–502.

    • Stuart, T. et al. (2019) Comprehensive Integration of Single-Cell Data. Cell, 177, 1888–1902.e21.

    • Hao, Y. et al. (2024) Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nat. Methods, 21, 1–9.

• Slingshot (trajectory inference)

  • web page: https://bioconductor.org/packages/release/bioc/html/slingshot.html

  • Publication:

    • Street, K. et al. (2018) Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics, 19, 477.

• scDblFinder (doublet detection)

  • web page: https://bioconductor.org/packages/release/bioc/html/scDblFinder.html

  • Publication:

    • Germain, P.-L. et al. (2022) Doublet identification in single-cell sequencing data using scDblFinder. F1000Res., 10, 979.

• SingleR (cell-type annotation)

  • web page: https://bioconductor.org/packages/release/bioc/html/SingleR.html

  • Publication:

    • Aran, D. et al. (2019) Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nat. Immunol., 20, 163–172.

• scMaSigPro (trajectory differential expression)

  • web page: https://github.com/BioBam/scMaSigPro

  • Publication:

    • Prieto, C. & Martínez-García, P.M. (2023) scMaSigPro: a polynomial regression framework for single-cell RNA sequencing time series. Bioinformatics, 39, btad681.

• harmony (batch integration)

  • web page: https://github.com/immunogenomics/harmony

  • Publication:

    • Korsunsky, I. et al. (2019) Fast, sensitive and accurate integration of single-cell data with Harmony. Nat. Methods, 16, 1289–1296.

• scCustomize

  • web page: https://samuel-marsh.github.io/scCustomize/

Additional packages

CRAN

• bslib: https://rstudio.github.io/bslib/

• DT: https://rstudio.github.io/DT/

• dplyr: https://dplyr.tidyverse.org/

• ggplot2: https://ggplot2.tidyverse.org/

• hdf5r: https://cran.r-project.org/web/packages/hdf5r/

• metap: https://cran.r-project.org/web/packages/metap/index.html

• patchwork: https://patchwork.data-imaginist.com/

• reactable: https://glin.github.io/reactable/

• reticulate: https://rstudio.github.io/reticulate/

• sass: https://rstudio.github.io/sass/

• shiny: https://shiny.posit.co/

• shinycssloaders: https://cran.r-project.org/web/packages/shinycssloaders/

• shinyFeedback: https://merlinoa.github.io/shinyFeedback/

• shinyWidgets: https://dreamrs.github.io/shinyWidgets/

• SeuratObject: https://cran.r-project.org/web/packages/SeuratObject/

Bioconductor

• celldex: https://bioconductor.org/packages/release/data/experiment/html/celldex.html

• SingleCellExperiment: https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html

• slingshot: https://bioconductor.org/packages/release/bioc/html/slingshot.html