library(Seurat)
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library(tidyverse)
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library(Matrix)
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library(RCurl)
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library(cowplot)
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library(AnnotationHub)
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## filter安装包
安装 CRAN 包：
install.packages("BiocManager")
BiocManager::install(c("tidyverse", "Matrix", "RCurl", "scales", "cowplot", "Seurat", "metap"))安装 Bioc 包：
测试包的安装
查看会话信息
R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] zh_CN.UTF-8/zh_CN.UTF-8/zh_CN.UTF-8/C/zh_CN.UTF-8/zh_CN.UTF-8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ensembldb_2.22.0 AnnotationFilter_1.22.0 GenomicFeatures_1.50.4
[4] AnnotationDbi_1.60.2 Biobase_2.58.0 GenomicRanges_1.50.2
[7] GenomeInfoDb_1.34.9 IRanges_2.32.0 S4Vectors_0.36.2
[10] AnnotationHub_3.6.0 BiocFileCache_2.6.1 dbplyr_2.3.2
[13] BiocGenerics_0.44.0 cowplot_1.1.1 scales_1.2.1
[16] RCurl_1.98-1.12 Matrix_1.5-4.1 lubridate_1.9.2
[19] forcats_1.0.0 stringr_1.5.0 dplyr_1.1.2
[22] purrr_1.0.1 readr_2.1.4 tidyr_1.3.0
[25] tibble_3.2.1 ggplot2_3.4.2 tidyverse_2.0.0
[28] SeuratObject_4.1.3 Seurat_4.3.0
loaded via a namespace (and not attached):
[1] utf8_1.2.3 spatstat.explore_3.2-1
[3] reticulate_1.28 tidyselect_1.2.0
[5] RSQLite_2.3.1 htmlwidgets_1.6.2
[7] grid_4.2.2 BiocParallel_1.32.6
[9] Rtsne_0.16 munsell_0.5.0
[11] codetools_0.2-19 ica_1.0-3
[13] future_1.32.0 miniUI_0.1.1.1
[15] withr_2.5.0 spatstat.random_3.1-5
[17] colorspace_2.1-0 progressr_0.13.0
[19] filelock_1.0.2 knitr_1.43
[21] rstudioapi_0.14 ROCR_1.0-11
[23] tensor_1.5 listenv_0.9.0
[25] MatrixGenerics_1.10.0 GenomeInfoDbData_1.2.9
[27] polyclip_1.10-4 bit64_4.0.5
[29] parallelly_1.36.0 vctrs_0.6.2
[31] generics_0.1.3 xfun_0.39
[33] timechange_0.2.0 R6_2.5.1
[35] bitops_1.0-7 spatstat.utils_3.0-3
[37] cachem_1.0.8 DelayedArray_0.24.0
[39] promises_1.2.0.1 BiocIO_1.8.0
[41] gtable_0.3.3 globals_0.16.2
[43] goftest_1.2-3 rlang_1.1.1
[45] splines_4.2.2 rtracklayer_1.58.0
[47] lazyeval_0.2.2 spatstat.geom_3.2-1
[49] BiocManager_1.30.20 yaml_2.3.7
[51] reshape2_1.4.4 abind_1.4-5
[53] httpuv_1.6.11 tools_4.2.2
[55] ellipsis_0.3.2 RColorBrewer_1.1-3
[57] ggridges_0.5.4 Rcpp_1.0.10
[59] plyr_1.8.8 progress_1.2.2
[61] zlibbioc_1.44.0 prettyunits_1.1.1
[63] deldir_1.0-9 pbapply_1.7-0
[65] zoo_1.8-12 SummarizedExperiment_1.28.0
[67] ggrepel_0.9.3 cluster_2.1.4
[69] magrittr_2.0.3 data.table_1.14.8
[71] scattermore_1.1 lmtest_0.9-40
[73] RANN_2.6.1 ProtGenerics_1.30.0
[75] fitdistrplus_1.1-11 matrixStats_0.63.0
[77] hms_1.1.3 patchwork_1.1.2
[79] mime_0.12 evaluate_0.21
[81] xtable_1.8-4 XML_3.99-0.14
[83] gridExtra_2.3 compiler_4.2.2
[85] biomaRt_2.54.1 KernSmooth_2.23-21
[87] crayon_1.5.2 htmltools_0.5.5
[89] later_1.3.1 tzdb_0.4.0
[91] DBI_1.1.3 MASS_7.3-60
[93] rappdirs_0.3.3 cli_3.6.1
[95] parallel_4.2.2 igraph_1.4.3
[97] pkgconfig_2.0.3 GenomicAlignments_1.34.1
[99] sp_1.6-0 plotly_4.10.1
[101] spatstat.sparse_3.0-1 xml2_1.3.4
[103] XVector_0.38.0 digest_0.6.31
[105] sctransform_0.3.5 RcppAnnoy_0.0.20
[107] spatstat.data_3.0-1 Biostrings_2.66.0
[109] rmarkdown_2.21 leiden_0.4.3
[111] uwot_0.1.14 restfulr_0.0.15
[113] curl_5.0.0 shiny_1.7.4
[115] Rsamtools_2.14.0 rjson_0.2.21
[117] lifecycle_1.0.3 nlme_3.1-162
[119] jsonlite_1.8.4 viridisLite_0.4.2
[121] fansi_1.0.4 pillar_1.9.0
[123] lattice_0.21-8 KEGGREST_1.38.0
[125] fastmap_1.1.1 httr_1.4.6
[127] survival_3.5-5 interactiveDisplayBase_1.36.0
[129] glue_1.6.2 png_0.1-8
[131] BiocVersion_3.16.0 bit_4.0.5
[133] stringi_1.7.12 blob_1.2.4
[135] memoise_2.0.1 irlba_2.3.5.1
[137] future.apply_1.11.0 阅读
接下来就可以阅读以下两份非常好的材料了解单细胞的预备知识。