http://cole-trapnell-lab.github.io/monocle-release/docs/为了使用DDRTree的降维方法，本文安装Monocle 2进行拟时间分析。
> BiocManager::version() [1] ‘3.13’
> sessionInfo() R version 4.1.1 (2021-08-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=zh_CN.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=zh_CN.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] splines stats4 parallel stats graphics grDevices utils [8] datasets methods base other attached packages: [1] monocle_2.9.0 DDRTree_0.1.5 irlba_2.3.5.1 [4] VGAM_1.1-7 ggplot2_3.4.0 Biobase_2.52.0 [7] BiocGenerics_0.38.0 Matrix_1.5-3 loaded via a namespace (and not attached): [1] tidyselect_1.2.0 slam_0.1-50 reshape2_1.4.4 [4] lattice_0.20-45 colorspace_2.0-3 vctrs_0.5.1 [7] generics_0.1.3 viridisLite_0.4.1 fastICA_1.2-3 [10] utf8_1.2.2 rlang_1.0.6 pillar_1.8.1 [13] glue_1.6.2 withr_2.5.0 DBI_1.1.3 [16] RColorBrewer_1.1-3 HSMMSingleCell_1.14.0 matrixStats_0.62.0 [19] lifecycle_1.0.3 plyr_1.8.8 stringr_1.4.1 [22] munsell_0.5.0 combinat_0.0-8 gtable_0.3.1 [25] fansi_1.0.3 Rcpp_1.0.9 BiocManager_1.30.19 [28] scales_1.2.1 limma_3.50.3 densityClust_0.3.2 [31] FNN_1.1.3.1 gridExtra_2.3 RANN_2.6.1 [34] stringi_1.7.8 Rtsne_0.16 sparsesvd_0.2-1 [37] qlcMatrix_0.9.7 dplyr_1.0.10 ggrepel_0.9.2 [40] grid_4.1.1 tools_4.1.1 cli_3.4.1 [43] magrittr_2.0.3 tibble_3.1.8 cluster_2.1.4 [46] pkgconfig_2.0.3 docopt_0.7.1 pheatmap_1.0.12 [49] viridis_0.6.2 assertthat_0.2.1 R6_2.5.1 [52] igraph_1.3.5 compiler_4.1.1
使用pip安装
pip
pip install pyscenic -i https://pypi.tuna.tsinghua.edu.cn/simple