Table 2. Software.
| Program | Version | Reference |
|---|---|---|
| Biobase | 2.52.0 | [98] |
| BiocGenerics | 0.38.0 | [98] |
| 10x Genomics Cell Ranger | 3.1.0 | [82] |
| clustree | 0.4.4 | [84] |
| corrplot | 0.90 | [99] |
| DBI | 1.1.1 | [100] |
| dbplyr | 2.1.1 | [101] |
| DelayedArray | 0.18.0 | [102] |
| DESeq2 | 1.32.0 | [86] |
| dplyr | 1.0.7 | [103] |
| eulerr | 6.1.1 | [94, 95] |
| ggplot2 | 3.3.5 | [104] |
| gprofiler2 | 0.2.1 | [44] |
| janitor | 2.1.0 | [105] |
| knitr | 2.0 | [106] |
| mixtools | 1.2.0 | [107] |
| openxlsx | 4.2.4 | [108] |
| patchwork | 1.1.1 | [109] |
| plyr | 1.8.6 | [110] |
| R | 4.1.1 | [111] |
| RColorBrewer | 1.1.2 | [112] |
| readr | 2.0.2 | [113] |
| RSQLite | 2.2.8 | [87] |
| Rstudio | 2021.09.1 | [93] |
| Salmon | 1.3.0 | [85] |
| Seurat | 4.0.5 | [83] |
| SRAtoolKit | 2.9.6 | [81] |
| stats | 4.1.1 | [111] |
| stringr | 1.4.0 | [114] |
| tidyverse | 1.3.1 | [115] |
| tximport | 1.20.0 | [116] |
| umap | 0.2.7.0 | [117] |
| viridisLite | 0.4.0 | [118] |
| 10x Genomics Loupe Browser | 4.1.0 | 10x Genomics, proprietary |