Single-nucleus RNA-seq data analysis of drprnull 42D vs. w1118 42D
> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: AlmaLinux 8.9 (Midnight Oncilla)
Matrix products: default
BLAS: /share/pkg.7/r/4.2.1/install/lib64/R/lib/libRblas.so
LAPACK: /share/pkg.7/r/4.2.1/install/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] scran_1.24.0 scater_1.24.0 scuttle_1.6.2
[4] robustbase_0.99-2 viridis_0.6.2 viridisLite_0.4.0
[7] SeuratObject_5.0.1 Seurat_4.1.1 reticulate_1.25
[10] SoupX_1.6.2 zellkonverter_1.6.5 singleCellTK_2.6.0
[13] DelayedArray_0.22.0 Matrix_1.6-5 forcats_0.5.1
[16] stringr_1.4.0 dplyr_1.0.9 purrr_0.3.4
[19] readr_2.1.2 tidyr_1.2.0 tibble_3.1.7
[22] ggplot2_3.3.6 tidyverse_1.3.1 SingleCellExperiment_1.18.0
[25] SummarizedExperiment_1.26.1 Biobase_2.56.0 GenomicRanges_1.48.0
[28] GenomeInfoDb_1.32.2 IRanges_2.30.0 S4Vectors_0.34.0
[31] BiocGenerics_0.42.0 MatrixGenerics_1.8.0 matrixStats_0.62.0
loaded via a namespace (and not attached):
[1] utf8_1.2.2 R.utils_2.11.0 tidyselect_1.1.2 htmlwidgets_1.5.4
[5] grid_4.2.1 BiocParallel_1.30.3 Rtsne_0.16 DropletUtils_1.16.0
[9] ScaledMatrix_1.4.0 munsell_0.5.0 codetools_0.2-18 ica_1.0-2
[13] statmod_1.4.36 future_1.26.1 miniUI_0.1.1.1 withr_2.5.0
[17] spatstat.random_3.2-3 colorspace_2.1-0 progressr_0.10.1 filelock_1.0.2
[21] rstudioapi_0.13 ROCR_1.0-11 tensor_1.5 listenv_0.8.0
[25] labeling_0.4.2 GenomeInfoDbData_1.2.8 GSVAdata_1.32.0 polyclip_1.10-0
[29] farver_2.1.0 rhdf5_2.40.0 basilisk_1.8.1 parallelly_1.32.0
[33] vctrs_0.4.1 generics_0.1.3 fishpond_2.2.0 R6_2.5.1
[37] ggbeeswarm_0.6.0 rsvd_1.0.5 locfit_1.5-9.5 bitops_1.0-7
[41] rhdf5filters_1.8.0 spatstat.utils_3.0-4 assertthat_0.2.1 promises_1.2.0.1
[45] scales_1.2.0 beeswarm_0.4.0 rgeos_0.5-9 gtable_0.3.0
[49] beachmat_2.12.0 globals_0.15.0 goftest_1.2-3 spam_2.8-0
[53] rlang_1.0.2 splines_4.2.1 lazyeval_0.2.2 spatstat.geom_3.2-9
[57] broom_0.8.0 reshape2_1.4.4 abind_1.4-7 modelr_0.1.8
[61] backports_1.4.1 httpuv_1.6.5 tools_4.2.1 ellipsis_0.3.2
[65] spatstat.core_2.4-4 RColorBrewer_1.1-3 ggridges_0.5.3 Rcpp_1.0.8.3
[69] plyr_1.8.7 sparseMatrixStats_1.8.0 zlibbioc_1.42.0 RCurl_1.98-1.7
[73] basilisk.utils_1.8.0 rpart_4.1.16 deldir_1.0-6 pbapply_1.5-0
[77] cowplot_1.1.1 zoo_1.8-10 haven_2.5.0 ggrepel_0.9.1
[81] cluster_2.1.3 fs_1.5.2 svMisc_1.2.3 magrittr_2.0.3
[85] RSpectra_0.16-1 data.table_1.14.2 scattermore_1.2 lmtest_0.9-40
[89] reprex_2.0.1 RANN_2.6.1 fitdistrplus_1.1-8 hms_1.1.1
[93] patchwork_1.1.0.9000 mime_0.12 xtable_1.8-6 readxl_1.4.0
[97] gridExtra_2.3 compiler_4.2.1 KernSmooth_2.23-20 crayon_1.5.1
[101] R.oo_1.25.0 htmltools_0.5.2 mgcv_1.8-40 later_1.3.0
[105] tzdb_0.3.0 lubridate_1.8.0 DBI_1.1.3 dbplyr_2.2.0
[109] MASS_7.3-57 cli_3.3.0 R.methodsS3_1.8.2 metapod_1.4.0
[113] parallel_4.2.1 dotCall64_1.0-1 igraph_1.3.2 pkgconfig_2.0.3
[117] dir.expiry_1.4.0 sp_1.5-0 plotly_4.10.0 spatstat.sparse_3.0-3
[121] xml2_1.3.3 vipor_0.4.5 dqrng_0.3.0 XVector_0.36.0
[125] rvest_1.0.2 digest_0.6.29 sctransform_0.4.1 RcppAnnoy_0.0.19
[129] spatstat.data_3.0-4 cellranger_1.1.0 leiden_0.4.2 uwot_0.1.11
[133] edgeR_3.38.1 DelayedMatrixStats_1.18.0 shiny_1.7.1 gtools_3.9.3
[137] lifecycle_1.0.1 nlme_3.1-158 jsonlite_1.8.0 Rhdf5lib_1.18.2
[141] BiocNeighbors_1.14.0 limma_3.52.2 fansi_1.0.3 pillar_1.7.0
[145] lattice_0.20-45 DEoptimR_1.0-11 fastmap_1.1.0 httr_1.4.3
[149] survival_3.3-1 glue_1.6.2 png_0.1-7 bluster_1.6.0
[153] stringi_1.7.6 HDF5Array_1.24.1 BiocSingular_1.12.0 irlba_2.3.5
[157] future.apply_1.9.0