单细胞分析

上游分析

Cell Ranger 10XGenomics/cellranger https://www.nature.com/articles/ncomms14049

RNA-seq

Packages

Code

# 按需安装
install.packages("BiocManager")
BiocManager::install("scater")
BiocManager::install("scuttle")
BiocManager::install("DropletUtils")
BiocManager::install("zellkonverter")
BiocManager::install("LoomExperiment")
BiocManager::install("SingleCellExperiment")
BiocManager::install("scran")
BiocManager::install("scRNAseq")
BiocManager::install("batchelor")
BiocManager::install("robustbase")
BiocManager::install("org.Mm.eg.db")
BiocManager::install("EnsDb.Hsapiens.v86")
BiocManager::install("mbkmeans")
BiocManager::install("SingleR")

Session Information

Code

Sys.Date()
#> [1] "2024-11-21"
BiocManager::version()
#> [1] '3.20'
BiocManager::valid()
#> [1] TRUE
devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.4.1 (2024-06-14 ucrt)
#>  os       Windows 11 x64 (build 22631)
#>  system   x86_64, mingw32
#>  ui       RTerm
#>  language en
#>  collate  Chinese (Simplified)_China.utf8
#>  ctype    Chinese (Simplified)_China.utf8
#>  tz       Asia/Shanghai
#>  date     2024-11-21
#>  pandoc   3.4 @ D:/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version  date (UTC) lib source
#>  BiocManager   1.30.25  2024-08-28 [1] CRAN (R 4.4.1)
#>  cachem        1.1.0    2024-05-16 [1] CRAN (R 4.4.1)
#>  cellranger    1.1.0    2016-07-27 [1] CRAN (R 4.4.1)
#>  cli           3.6.3    2024-06-21 [1] CRAN (R 4.4.1)
#>  colorspace    2.1-1    2024-07-26 [1] CRAN (R 4.4.1)
#>  conflicted  * 1.2.0    2023-02-01 [1] CRAN (R 4.4.1)
#>  devtools      2.4.5    2022-10-11 [1] CRAN (R 4.4.1)
#>  digest        0.6.37   2024-08-19 [1] CRAN (R 4.4.1)
#>  dplyr       * 1.1.4    2023-11-17 [1] CRAN (R 4.4.1)
#>  ellipsis      0.3.2    2021-04-29 [1] CRAN (R 4.4.1)
#>  evaluate      1.0.1    2024-10-10 [1] CRAN (R 4.4.1)
#>  fansi         1.0.6    2023-12-08 [1] CRAN (R 4.4.1)
#>  fastmap       1.2.0    2024-05-15 [1] CRAN (R 4.4.1)
#>  forcats     * 1.0.0    2023-01-29 [1] CRAN (R 4.4.1)
#>  fs            1.6.5    2024-10-30 [1] CRAN (R 4.4.1)
#>  generics      0.1.3    2022-07-05 [1] CRAN (R 4.4.1)
#>  ggplot2     * 3.5.1    2024-04-23 [1] CRAN (R 4.4.1)
#>  glue          1.8.0    2024-09-30 [1] CRAN (R 4.4.1)
#>  gtable        0.3.6    2024-10-25 [1] CRAN (R 4.4.1)
#>  hms           1.1.3    2023-03-21 [1] CRAN (R 4.4.1)
#>  htmltools     0.5.8.1  2024-04-04 [1] CRAN (R 4.4.1)
#>  htmlwidgets   1.6.4    2023-12-06 [1] CRAN (R 4.4.1)
#>  httpuv        1.6.15   2024-03-26 [1] CRAN (R 4.4.1)
#>  jsonlite      1.8.9    2024-09-20 [1] CRAN (R 4.4.1)
#>  knitr         1.49     2024-11-08 [1] CRAN (R 4.4.2)
#>  later         1.3.2    2023-12-06 [1] CRAN (R 4.4.1)
#>  lifecycle     1.0.4    2023-11-07 [1] CRAN (R 4.4.1)
#>  lubridate   * 1.9.3    2023-09-27 [1] CRAN (R 4.4.1)
#>  magrittr      2.0.3    2022-03-30 [1] CRAN (R 4.4.1)
#>  memoise       2.0.1    2021-11-26 [1] CRAN (R 4.4.1)
#>  mime          0.12     2021-09-28 [1] CRAN (R 4.4.0)
#>  miniUI        0.1.1.1  2018-05-18 [1] CRAN (R 4.4.1)
#>  munsell       0.5.1    2024-04-01 [1] CRAN (R 4.4.1)
#>  pillar        1.9.0    2023-03-22 [1] CRAN (R 4.4.1)
#>  pkgbuild      1.4.5    2024-10-28 [1] CRAN (R 4.4.1)
#>  pkgconfig     2.0.3    2019-09-22 [1] CRAN (R 4.4.1)
#>  pkgload       1.4.0    2024-06-28 [1] CRAN (R 4.4.1)
#>  profvis       0.4.0    2024-09-20 [1] CRAN (R 4.4.1)
#>  promises      1.3.0    2024-04-05 [1] CRAN (R 4.4.1)
#>  purrr       * 1.0.2    2023-08-10 [1] CRAN (R 4.4.1)
#>  R6            2.5.1    2021-08-19 [1] CRAN (R 4.4.1)
#>  Rcpp          1.0.13-1 2024-11-02 [1] CRAN (R 4.4.1)
#>  readr       * 2.1.5    2024-01-10 [1] CRAN (R 4.4.1)
#>  readxl      * 1.4.3    2023-07-06 [1] CRAN (R 4.4.1)
#>  remotes       2.5.0    2024-03-17 [1] CRAN (R 4.4.1)
#>  rlang         1.1.4    2024-06-04 [1] CRAN (R 4.4.1)
#>  rmarkdown     2.29     2024-11-04 [1] CRAN (R 4.4.1)
#>  rstudioapi    0.17.1   2024-10-22 [1] CRAN (R 4.4.1)
#>  scales        1.3.0    2023-11-28 [1] CRAN (R 4.4.1)
#>  sessioninfo   1.2.2    2021-12-06 [1] CRAN (R 4.4.1)
#>  shiny         1.9.1    2024-08-01 [1] CRAN (R 4.4.1)
#>  showtext    * 0.9-7    2024-03-02 [1] CRAN (R 4.4.1)
#>  showtextdb  * 3.0      2020-06-04 [1] CRAN (R 4.4.1)
#>  stringi       1.8.4    2024-05-06 [1] CRAN (R 4.4.0)
#>  stringr     * 1.5.1    2023-11-14 [1] CRAN (R 4.4.1)
#>  sysfonts    * 0.8.9    2024-03-02 [1] CRAN (R 4.4.1)
#>  tibble      * 3.2.1    2023-03-20 [1] CRAN (R 4.4.1)
#>  tidyr       * 1.3.1    2024-01-24 [1] CRAN (R 4.4.1)
#>  tidyselect    1.2.1    2024-03-11 [1] CRAN (R 4.4.1)
#>  tidyverse   * 2.0.0    2023-02-22 [1] CRAN (R 4.4.1)
#>  timechange    0.3.0    2024-01-18 [1] CRAN (R 4.4.1)
#>  tzdb          0.4.0    2023-05-12 [1] CRAN (R 4.4.1)
#>  urlchecker    1.0.1    2021-11-30 [1] CRAN (R 4.4.1)
#>  usethis       3.0.0    2024-07-29 [1] CRAN (R 4.4.1)
#>  utf8          1.2.4    2023-10-22 [1] CRAN (R 4.4.1)
#>  vctrs         0.6.5    2023-12-01 [1] CRAN (R 4.4.1)
#>  withr         3.0.2    2024-10-28 [1] CRAN (R 4.4.1)
#>  writexl     * 1.5.1    2024-10-04 [1] CRAN (R 4.4.1)
#>  xfun          0.49     2024-10-31 [1] CRAN (R 4.4.1)
#>  xtable        1.8-4    2019-04-21 [1] CRAN (R 4.4.1)
#>  yaml          2.3.10   2024-07-26 [1] CRAN (R 4.4.1)
#> 
#>  [1] D:/R-4.4.1/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────