references.rst

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

Three packages are the analytical core of Asc-Seurat. Below is listed their information.

• 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.

• Dynverse (dynplot, dynwrap, and dynfeature)

  • web page: https://dynverse.org/
  • Publications:
    • Saelens, W. et al. (2019) A comparison of single-cell trajectory inference methods. Nat. Biotechnol., 37, 547–554.

• biomaRt

  • web page: https://bioconductor.org/packages/release/bioc/html/biomaRt.html
  • Publications:
    • Durinck, S. et al. (2009) Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat. Protoc., 4, 1184–1191.

Additional packages

CRAN

• circlize: https://cran.r-project.org/web/packages/circlize/
• DT: https://cran.r-project.org/web/packages/DT/
• dplyr: https://mran.microsoft.com/web/packages/dplyr/index.html
• future: https://cran.r-project.org/web/packages/future/index.html
• ggplot2: https://cran.r-project.org/web/packages/ggplot2/index.html
• ggthemes: https://cran.r-project.org/web/packages/ggthemes/index.html
• hdf5r: https://cran.r-project.org/web/packages/hdf5r/
• metap: https://cran.r-project.org/web/packages/metap/index.html
• patchwork: https://cran.r-project.org/web/packages/patchwork/index.html
• rclipboard: https://cran.r-project.org/web/packages/rclipboard/index.html
• reactable: https://cran.r-project.org/web/packages/reactable/index.html
• scales: https://cran.r-project.org/web/packages/scales/index.html
• sctransform: https://cran.r-project.org/web/packages/sctransform/index.html
• SeuratObject: https://cran.r-project.org/web/packages/SeuratObject/index.html
• shiny: https://cran.r-project.org/web/packages/shiny/index.html
• shinycssloaders: https://cran.r-project.org/web/packages/shinycssloaders/index.html
• shinyFeedback: https://cran.r-project.org/web/packages/shinyFeedback/index.html
• shinyWidgets: https://cran.r-project.org/web/packages/shinyWidgets/index.html
• tidyverse: https://cran.r-project.org/web/packages/tidyverse/index.html
• utils: https://cran.r-project.org/web/packages/R.utils/index.html

Bioconductor

• ComplexHeatmap: https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html
• glmGamPoi: https://bioconductor.org/packages/release/bioc/html/glmGamPoi.html
• multtest: https://bioconductor.org/packages/release/bioc/html/multtest.html
• SingleCellExperiment: https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html
• slingshot: https://bioconductor.org/packages/release/bioc/html/slingshot.html
• topGO: https://bioconductor.org/packages/release/bioc/html/topGO.html
• tradeSeq: https://bioconductor.org/packages/release/bioc/html/tradeSeq.html