| R Studio | https://www.rstudio.com/products/rstudio/download/ |
| R, latest version | https://cran.r-project.org/ |
| Covid data, sample C143 | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4339771 |
| Covid data, sample C145 | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4339773 |
| Covid data, sample C51 | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4475048 |
| Covid data, sample C52 | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4475049 |
| R package SingleCellExperiment | https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html |
| R package Matrix | https://cran.r-project.org/web/packages/Matrix/index.html |
| R package DropletUtils | https://bioconductor.org/packages/release/bioc/html/DropletUtils.html |
| R package scran | https://bioconductor.org/packages/release/bioc/html/scran.html |
| R package batchelor | https://www.bioconductor.org/packages/release/bioc/html/batchelor.html |
| R package Seurat | https://cran.r-project.org/web/packages/Seurat/index.html |
| R package uwot | https://github.com/jlmelville/uwot |
| R package dplyr | https://cran.r-project.org/web/packages/dplyr/index.html |
| R package irlba | https://cran.r-project.org/web/packages/irlba/index.html |
| R package miloR (development version) | https://github.com/MarioniLab/miloR |
| R package stringr | https://cran.r-project.org/web/packages/stringr/index.html |
| R package gdata | https://cran.r-project.org/web/packages/gdata/index.html |
| R package DoubletFinder | https://github.com/chris-mcginnis-ucsf/DoubletFinder |
| R package ggplot2 | https://ggplot2.tidyverse.org/ |
| R package ggpubr | https://cran.r-project.org/web/packages/ggpubr/index.html |
| R package MouseGastrulationData | https://bioconductor.org/packages/release/data/experiment/html/MouseGastrulationData.html |
| R package viridis | https://cran.r-project.org/web/packages/viridis/index.html |
| Magick++ | https://imagemagick.org/Magick++/ |
| R package igraph | https://cran.r-project.org/web/packages/igraph/index.html |
| R package celldex | http://bioconductor.org/packages/release/data/experiment/html/celldex.html |
| R package SingleR | https://bioconductor.org/packages/release/bioc/html/SingleR.html |
| R package pheatmap | https://cran.r-project.org/web/packages/pheatmap/index.html |
| R package SC3 | https://www.bioconductor.org/packages/release/bioc/html/SC3.html |
| R package Harmony | https://cran.r-project.org/web/packages/harmony/index.html |
| R package Seurat | https://cran.r-project.org/web/packages/Seurat/index.html |
| R package Azimuth | https://github.com/satijalab/azimuth |
| R package SeuratData | https://github.com/satijalab/seurat-data |
| R package patchwork | https://cran.r-project.org/web/packages/patchwork/index.html |
| R package bluster | https://bioconductor.org/packages/3.15/bioc/html/bluster.html |
| R package scater | https://bioconductor.org/packages/release/bioc/html/scater.html |
