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.