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¶
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
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