Installation ------------ Requirements ^^^^^^^^^^^^ EpiTrace requires R 4.0 or later. The current recommended environment is R 4.1.3. You will need a **working compiler** and working internet connection in an environment where you can successfully install ``Seurat`` and ``Signac`` (most dependencies coming from Seurat). We have tested installation of EpiTrace in freshly-installed R-4.3.2 on MacOS with XCODE supplied ``clang``, and R-4.2.0 on Linux, using the following steps. **Installation on Windows has not been tested**. Simple install ^^^^^^^^^^^^^^ We recommend to install EpiTrace using ``pak``. It seems that ``pak`` handles dependencies hosted on different sources well. Install EpiTrace from Github using:: if(!require(pak)){ install.packages("pak") } library(pak) pak::pkg_install('caleblareau/easyLift') pak::pkg_install('MagpiePKU/EpiTrace') If you encountered any issue in installation, please let us know by flagging up an issue `here in Github `_. Dependencies ^^^^^^^^^^^^ - dplyr - tidyr - RColorBrewer - ggplot2 - Seurat (>=4.0) - SeuratObject - Signac (>= 1.5.0) - GenomicRanges - plyranges (>= 1.0) - WGCNA (>= 1.7) - stringr - easyLift - parallel - nnls - ggtree - ape - reticulate - ggpubr - Matrix - matrixStats - sparseMatrixStats - plyranges Example installation log ^^^^^^^^^^^^^^^^^^^^^^^^ Fresh installation on a newly installed R:: > pak::pkg_install('MagpiePKU/EpiTrace') ✔ Updated metadata database: 2.86 MB in 8 files. ✔ Updating metadata database ... done → Will install 223 packages. → Will update 1 package. → Will download 203 CRAN packages (163.12 MB). → Will download 21 packages with unknown size. + AnnotationDbi 1.64.1 👷🏾 ⬇ + BH 1.84.0-0 👷🏽‍♀️ ⬇ (14.02 MB) + Biobase 2.62.0 👷🏼‍♀️🔧 ⬇ + BiocGenerics 0.48.1 👷🏻 ⬇ .... ℹ Packaging EpiTrace 0.0.1.3 ✔ Packaged EpiTrace 0.0.1.3 (5.9s) ℹ Building EpiTrace 0.0.1.3 ✔ Built EpiTrace 0.0.1.3 (41.6s) ✔ Installed EpiTrace 0.0.1.3 (github::MagpiePKU/EpiTrace@38d36a6) (251ms) ✔ 1 pkg + 227 deps: kept 220, added 1, dld 1 (NA B) [1m 20.9s] Example session info ^^^^^^^^^^^^^^^^^^^^ **Developer environment**:: > sessionInfo() R version 4.2.0 (2022-04-22) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS 14.2 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib locale: [1] C/UTF-8/C/C/C/C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] ggpubr_0.4.0 reticulate_1.25 ape_5.7-1 [4] ggtree_3.4.0 nnls_1.4 HiClimR_2.2.1 [7] ccaPP_0.3.3 robustbase_0.95-0 pcaPP_2.0-1 [10] sva_3.44.0 BiocParallel_1.30.2 genefilter_1.78.0 [13] mgcv_1.8-40 nlme_3.1-157 easyLift_0.2.1 [16] stringr_1.4.0 WGCNA_1.71 fastcluster_1.2.3 [19] dynamicTreeCut_1.63-1 plyranges_1.16.0 GenomicRanges_1.48.0 [22] GenomeInfoDb_1.34.9 IRanges_2.30.0 S4Vectors_0.34.0 [25] BiocGenerics_0.42.0 ggplot2_3.3.6 RColorBrewer_1.1-3 [28] tidyr_1.2.0 dplyr_1.1.4 Signac_1.6.0 [31] sp_1.4-7 SeuratObject_4.1.0 Seurat_4.1.1 [34] EpiTrace_0.0.0.9000 **Tested installation environment**:: > sessionInfo() R version 4.3.2 (2023-10-31) Platform: aarch64-apple-darwin23.2.0 (64-bit) Running under: macOS Sonoma 14.2 Matrix products: default BLAS: /Users/wing/Desktop/Eulerian/文件/内部研发项目/CLOCK_CANCER/Clock_Evolution/test_install/R-4.3.2/lib/libRblas.dylib LAPACK: /Users/wing/Desktop/Eulerian/文件/内部研发项目/CLOCK_CANCER/Clock_Evolution/test_install/R-4.3.2/lib/libRlapack.dylib; LAPACK version 3.11.0 locale: [1] C/UTF-8/C/C/C/C time zone: Asia/Shanghai tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] EpiTrace_0.0.1.3 pak_0.7.1 loaded via a namespace (and not attached): [1] RcppAnnoy_0.0.22 splines_4.3.2 [3] later_1.3.2 BiocIO_1.12.0 [5] ggplotify_0.1.2 bitops_1.0-7 [7] easyLift_0.2.1 tibble_3.2.1 [9] polyclip_1.10-6 preprocessCore_1.64.0 [11] rpart_4.1.21 XML_3.99-0.16.1 [13] fastDummies_1.7.3 lifecycle_1.0.4 [15] fastcluster_1.2.6 doParallel_1.0.17 [17] globals_0.16.2 lattice_0.21-9 [19] MASS_7.3-60 backports_1.4.1 [21] magrittr_2.0.3 rmarkdown_2.25 [23] Hmisc_5.1-1 plotly_4.10.4 [25] yaml_2.3.8 httpuv_1.6.14 [27] Seurat_5.0.1 sctransform_0.4.1 [29] spam_2.10-0 sp_2.1-2 [31] spatstat.sparse_3.0-3 reticulate_1.34.0 [33] cowplot_1.1.3 pbapply_1.7-2 [35] DBI_1.2.1 RColorBrewer_1.1-3 [37] abind_1.4-5 zlibbioc_1.48.0 [39] Rtsne_0.17 GenomicRanges_1.54.1 [41] purrr_1.0.2 BiocGenerics_0.48.1 [43] RCurl_1.98-1.14 yulab.utils_0.1.3 [45] nnet_7.3-19 GenomeInfoDbData_1.2.11 [47] IRanges_2.36.0 S4Vectors_0.40.2 [49] ggrepel_0.9.5 irlba_2.3.5.1 [51] listenv_0.9.0 spatstat.utils_3.0-4 [53] tidytree_0.4.6 goftest_1.2-3 [55] RSpectra_0.16-1 spatstat.random_3.2-2 [57] fitdistrplus_1.1-11 parallelly_1.36.0 [59] leiden_0.4.3.1 codetools_0.2-19 [61] DelayedArray_0.28.0 RcppRoll_0.3.0 [63] tidyselect_1.2.0 aplot_0.2.2 [65] base64enc_0.1-3 matrixStats_1.2.0 [67] stats4_4.3.2 dynamicTreeCut_1.63-1 [69] spatstat.explore_3.2-5 GenomicAlignments_1.38.2 [71] jsonlite_1.8.8 Formula_1.2-5 [73] ellipsis_0.3.2 progressr_0.14.0 [75] ggridges_0.5.6 survival_3.5-7 [77] iterators_1.0.14 foreach_1.5.2 [79] tools_4.3.2 treeio_1.26.0 [81] ica_1.0-3 Rcpp_1.0.12 [83] glue_1.7.0 gridExtra_2.3 [85] SparseArray_1.2.3 xfun_0.41 [87] MatrixGenerics_1.14.0 GenomeInfoDb_1.38.5 [89] dplyr_1.1.4 fastmap_1.1.1 [91] fansi_1.0.6 digest_0.6.34 [93] gridGraphics_0.5-1 R6_2.5.1 [95] mime_0.12 colorspace_2.1-0 [97] scattermore_1.2 GO.db_3.18.0 [99] tensor_1.5 RSQLite_2.3.5 [101] spatstat.data_3.0-4 utf8_1.2.4 [103] tidyr_1.3.1 generics_0.1.3 [105] data.table_1.14.10 rtracklayer_1.62.0 [107] httr_1.4.7 htmlwidgets_1.6.4 [109] S4Arrays_1.2.0 uwot_0.1.16 [111] pkgconfig_2.0.3 gtable_0.3.4 [113] blob_1.2.4 impute_1.76.0 [115] lmtest_0.9-40 XVector_0.42.0 [117] htmltools_0.5.7 dotCall64_1.1-1 [119] plyranges_1.22.0 SeuratObject_5.0.1 [121] scales_1.3.0 Biobase_2.62.0 [123] png_0.1-8 ggfun_0.1.4 [125] rstudioapi_0.15.0 knitr_1.45 [127] Signac_1.12.0 reshape2_1.4.4 [129] rjson_0.2.21 checkmate_2.3.1 [131] nlme_3.1-163 cachem_1.0.8 [133] zoo_1.8-12 stringr_1.5.1 [135] KernSmooth_2.23-22 parallel_4.3.2 [137] miniUI_0.1.1.1 foreign_0.8-85 [139] AnnotationDbi_1.64.1 restfulr_0.0.15 [141] pillar_1.9.0 grid_4.3.2 [143] vctrs_0.6.5 RANN_2.6.1 [145] promises_1.2.1 xtable_1.8-4 [147] cluster_2.1.4 htmlTable_2.4.2 [149] evaluate_0.23 cli_3.6.2 [151] compiler_4.3.2 Rsamtools_2.18.0 [153] rlang_1.1.3 crayon_1.5.2 [155] future.apply_1.11.1 fs_1.6.3 [157] plyr_1.8.9 stringi_1.8.3 [159] nnls_1.5 viridisLite_0.4.2 [161] deldir_2.0-2 WGCNA_1.72-5 [163] BiocParallel_1.36.0 munsell_0.5.0 [165] Biostrings_2.70.1 lazyeval_0.2.2 [167] spatstat.geom_3.2-8 Matrix_1.6-5 [169] RcppHNSW_0.5.0 patchwork_1.2.0 [171] bit64_4.0.5 future_1.33.1 [173] ggplot2_3.4.4 KEGGREST_1.42.0 [175] shiny_1.8.0 SummarizedExperiment_1.32.0 [177] ROCR_1.0-11 memoise_2.0.1 [179] igraph_1.6.0 ggtree_3.10.0 [181] fastmatch_1.1-4 bit_4.0.5 [183] ape_5.7-1 Again, if you run into issues in installation or using, do not hesitate to approach us or raise a `GitHub issue`_. .. _Github: https://github.com/MagpiePKU/EpiTrace .. _`Github issue`: https://github.com/MagpiePKU/EpiTrace/issues/new