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DCIS TME

This repository contains the scripts used in the DCIS TME project.

Session Information

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