| Deposited data |
|
| scRNA sequencing analysis for human ureters and patient derived ureter organoid |
Angela Ting1
|
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE184111 |
| Protocol sample data |
This paper |
https://github.com/matthewdbradley/sge-integration/releases/tag/V1 |
|
| Software and algorithms |
|
| R (v4.1.2) |
https://www.r-project.org/ |
https://www.r-project.org/ |
| Seurat (v4.2.0) |
https://satijalab.org/seurat/ |
https://satijalab.org/seurat/ |
| dplyr (v1.0.8) |
https://dplyr.tidyverse.org/ |
https://dplyr.tidyverse.org/ |
| tidyverse (v1.3.1) |
https://www.tidyverse.org/ |
https://www.tidyverse.org/ |
| purr (v0.3.4) |
https://purrr.tidyverse.org/ |
https://purrr.tidyverse.org/ |
| janitor (v2.1.0) |
https://cran.r-project.org/web/packages/janitor/vignettes/janitor.html |
https://cran.r-project.org/web/packages/janitor/vignettes/janitor.html |
| magrittr (v2.0.2) |
https://cran.r-project.org/web/packages/magrittr/vignettes/magrittr.html |
https://cran.r-project.org/web/packages/magrittr/vignettes/magrittr.html |
| patchwork (v1.1.1) |
https://patchwork.data-imaginist.com/ |
https://patchwork.data-imaginist.com/ |
| Giotto (v1.1.0) |
https://giottosuite.readthedocs.io/en/master/ |
https://giottosuite.readthedocs.io/en/master/ |
| ggplot2 (v3.3.6) |
https://ggplot2.tidyverse.org/ |
https://ggplot2.tidyverse.org/ |
| viridis (v0.6.2) |
https://cran.r-project.org/web/packages/viridis/vignettes/intro-to-viridis.html |
https://cran.r-project.org/web/packages/viridis/vignettes/intro-to-viridis.html |
| Matrix (v1.4-0) |
https://cran.r-project.org/web/packages/Matrix/index.html |
https://cran.r-project.org/web/packages/Matrix/index.html |
| igraph (v1.3.1) |
https://igraph.org/r/ |
https://igraph.org/r/ |
| RColorBrewer (v1.1-3) |
https://r-graph-gallery.com/38-rcolorbrewers-palettes.html |
https://r-graph-gallery.com/38-rcolorbrewers-palettes.html |
| shiny (v1.7.1) |
https://shiny.rstudio.com/ |
https://shiny.rstudio.com/ |
| miniUI (v1.1.1.1) |
https://cran.r-project.org/web/packages/miniUI/index.html |
https://cran.r-project.org/web/packages/miniUI/index.html |
| layer (v0.0.1) |
https://cran.r-project.org/web/packages/layer/index.html |
https://cran.r-project.org/web/packages/layer/index.html |
| grid (v4.0.3) |
https://bookdown.org/rdpeng/RProgDA/the-grid-package.html |
https://bookdown.org/rdpeng/RProgDA/the-grid-package.html |
| Cairo (v1.5-15) |
https://cran.r-project.org/web/packages/Cairo/index.html |
https://cran.r-project.org/web/packages/Cairo/index.html |
| stringr (v1.5.0) |
https://cloud.r-project.org/web/packages/stringr/index.html |
https://cloud.r-project.org/web/packages/stringr/index.html |
| R.utils (v2.12) |
https://cran.r-project.org/web/packages/R.utils/index.html |
https://cran.r-project.org/web/packages/R.utils/index.html |
| remotes (v2.4.2) |
https://cran.r-project.org/web/packages/remotes/index.html |
https://cran.r-project.org/web/packages/remotes/index.html |
| devtools (2.4.5) |
https://cran.r-project.org/web/packages/devtools/index.html |
https://cran.r-project.org/web/packages/devtools/index.html |
| Analysis code on Github |
This paper |
https://github.com/tingalab/sge-integration, Zenodo https://doi.org/10.5281/zenodo.7471053https://zenodo.org/account/settings/github/repository/tingalab/sge-integration
|
|
| Other |
|
| Hardware requirement |
We recommend a machine with at least 64 GB of memory. However, utilizing up to around 100–128 GB can still beneficial. We recommend performing this protocol with at least 8 CPU cores. We ran ours with 32 cores |
