This repository contains the scripts used in the DCIS TME project.
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8
[8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] org.Hs.eg.db_3.14.0 AnnotationDbi_1.56.2 stringr_1.5.1 clusterProfiler_4.2.2 cowplot_1.1.3 ggalluvial_0.12.3 ktplots_2.3.0
[8] Matrix_1.6-5 sceasy_0.0.7 reticulate_1.28 shiny_1.8.0 SeuratWrappers_0.3.0 harmony_1.1.0 Rcpp_1.0.12
[15] igraph_1.5.1 survival_3.3-0 survminer_0.4.9 bigmemory_4.5.36 ggraph_2.1.0 Nebulosa_1.4.0 patchwork_1.2.0
[22] reshape2_1.4.4 ggpubr_0.6.0 ggplot2_3.5.0 SeuratObject_5.0.1 Seurat_4.3.0 tidyr_1.3.1 ComplexHeatmap_2.10.0
[29] magrittr_2.0.3 paletteer_1.4.0 wesanderson_0.3.7 dplyr_1.1.4 RColorBrewer_1.1-3 SCENIC_1.3.1 AUCell_1.16.0
[36] destiny_3.8.1 spacexr_2.0.0 slingshot_2.2.1 princurve_2.1.6 TrajectoryUtils_1.2.0 SingleCellExperiment_1.16.0 SummarizedExperiment_1.24.0
[43] Biobase_2.54.0 GenomicRanges_1.46.1 GenomeInfoDb_1.30.1 IRanges_2.28.0 S4Vectors_0.32.4 BiocGenerics_0.40.0 MatrixGenerics_1.6.0
[50] matrixStats_1.2.0