Code and Data accompanying the HD-MIBI paper https://www.nature.com/articles/s41467-021-24822-1
This R notebook was written and executed on a custom built server with the following specifications. 2 x Intel(R) Xeon(R) CPU E5-2650 12 x 32GB Ram
The R sessioninfo is as follows: R version 3.5.3 (2019-03-11) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.6 LTS
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] fastcluster_1.1.25 spatstat_1.58-2 rpart_4.1-13
[4] nlme_3.1-137 spatstat.data_1.4-0 gridExtra_2.3
[7] RColorBrewer_1.1-2 Rtsne_0.15 gplots_3.0.1.1
[10] ggplot2_3.1.0 bioimagetools_1.1.3
loaded via a namespace (and not attached):
[1] gtools_3.8.1 tidyselect_0.2.5 locfit_1.5-9.1
[4] xfun_0.4 purrr_0.3.0 splines_3.5.3
[7] lattice_0.20-38 colorspace_1.4-0 spatstat.utils_1.13-0
[10] htmltools_0.3.6 mgcv_1.8-27 rlang_0.4.0
[13] pillar_1.3.1 glue_1.3.0 withr_2.1.2
[16] EBImage_4.24.0 BiocGenerics_0.28.0 jpeg_0.1-8
[19] plyr_1.8.4 munsell_0.5.0 gtable_0.2.0
[22] htmlwidgets_1.3 caTools_1.17.1.2 knitr_1.21
[25] Rcpp_1.0.2 tensor_1.5 KernSmooth_2.23-15
[28] scales_1.0.0 gdata_2.18.0 abind_1.4-5
[31] deldir_0.1-16 png_0.1-7 digest_0.6.18
[34] tiff_0.1-5 dplyr_0.8.3 polyclip_1.9-1
[37] grid_3.5.3 tools_3.5.3 bitops_1.0-6
[40] magrittr_1.5 goftest_1.1-1 lazyeval_0.2.1
[43] RCurl_1.95-4.11 tibble_2.0.1 crayon_1.3.4
[46] pkgconfig_2.0.2 Matrix_1.2-15 assertthat_0.2.0
[49] httr_1.4.0 rstudioapi_0.9.0 R6_2.3.0
[52] fftwtools_0.9-8 compiler_3.5.3
The following packages will be needed to execute the R notebook. The exact versions are listed above. - bioimagetools - ggplot2 - gplots - Rtsne - RColorBrewer - gridExtra - spatstat - parallel - fastcluster
Additional custom functions called upon are provided in "srIBI_functions.R"
Step by step instructions, along with data related to this manuscript, are provided in the R notebook: "Submission_Extract_Features_5_Cells_largervoxels.Rmd"
Raw Data is available here: https://www.dropbox.com/sh/dyusn5omopxd4yp/AAARXa00gQml9jaaWSqCV0UUa?dl=0