单细胞软件安装

monocle软件安装

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    

SCENIC-Python安装

使用pip安装

pip install pyscenic -i https://pypi.tuna.tsinghua.edu.cn/simple