You can install scMEGA via below commands:
# Install devtools
if (!requireNamespace("devtools", quietly = TRUE))
install.packages("devtools")
# First install Seurate v5
devtools::install_github("satijalab/seurat", "seurat5", upgrade='always')## Skipping install of 'Seurat' from a github remote, the SHA1 (f6ec683a) has not changed since last install.
## Use `force = TRUE` to force installation# Install scMEGA
devtools::install_github("CostaLab/scMEGA")## Skipping install of 'scMEGA' from a github remote, the SHA1 (fb5e54d9) has not changed since last install.
## Use `force = TRUE` to force installation# Check session information
sessionInfo()## R version 4.2.1 (2022-06-23)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] scMEGA_1.0.1
##
## loaded via a namespace (and not attached):
## [1] utf8_1.2.3 spatstat.explore_3.2-1 reticulate_1.30 tidyselect_1.2.0
## [5] htmlwidgets_1.6.2 grid_4.2.1 ranger_0.14.1 Rtsne_0.16
## [9] devtools_2.4.5 munsell_0.5.0 destiny_3.10.0 codetools_0.2-19
## [13] ica_1.0-3 future_1.33.0 miniUI_0.1.1.1 withr_2.5.0
## [17] spatstat.random_3.1-5 colorspace_2.1-0 progressr_0.13.0 Biobase_2.58.0
## [21] knitr_1.43 rstudioapi_0.14 Seurat_4.9.9.9058 stats4_4.2.1
## [25] SingleCellExperiment_1.20.1 ROCR_1.0-11 robustbase_0.95-0 vcd_1.4-11
## [29] tensor_1.5 VIM_6.2.2 TTR_0.24.3 listenv_0.9.0
## [33] MatrixGenerics_1.10.0 GenomeInfoDbData_1.2.9 polyclip_1.10-4 farver_2.1.1
## [37] rprojroot_2.0.3 parallelly_1.36.0 vctrs_0.6.3 generics_0.1.3
## [41] xfun_0.39 ggthemes_4.2.4 R6_2.5.1 GenomeInfoDb_1.34.9
## [45] graphlayouts_1.0.0 RcppEigen_0.3.3.9.3 cachem_1.0.8 bitops_1.0-7
## [49] spatstat.utils_3.0-3 DelayedArray_0.24.0 promises_1.2.0.1 scales_1.2.1
## [53] ggraph_2.1.0 nnet_7.3-18 gtable_0.3.3 globals_0.16.2
## [57] processx_3.8.2 goftest_1.2-3 spam_2.9-1 tidygraph_1.2.3
## [61] rlang_1.1.1 scatterplot3d_0.3-44 splines_4.2.1 lazyeval_0.2.2
## [65] hexbin_1.28.2 spatstat.geom_3.2-1 yaml_2.3.7 reshape2_1.4.4
## [69] abind_1.4-5 httpuv_1.6.11 usethis_2.1.6 tools_4.2.1
## [73] ggplot2_3.4.2 ellipsis_0.3.2 jquerylib_0.1.4 RColorBrewer_1.1-3
## [77] proxy_0.4-27 BiocGenerics_0.44.0 sessioninfo_1.2.2 ggridges_0.5.4
## [81] Rcpp_1.0.11 plyr_1.8.8 zlibbioc_1.44.0 purrr_1.0.1
## [85] RCurl_1.98-1.12 prettyunits_1.1.1 ps_1.7.5 deldir_1.0-9
## [89] pbapply_1.7-0 viridis_0.6.4 urlchecker_1.0.1 cowplot_1.1.1
## [93] S4Vectors_0.36.2 zoo_1.8-12 SeuratObject_4.9.9.9091 SummarizedExperiment_1.28.0
## [97] ggrepel_0.9.3 cluster_2.1.4 fs_1.6.3 factoextra_1.0.7
## [101] magrittr_2.0.3 data.table_1.14.8 RSpectra_0.16-1 scattermore_1.2
## [105] lmtest_0.9-40 RANN_2.6.1 pcaMethods_1.88.0 fitdistrplus_1.1-11
## [109] matrixStats_1.0.0 pkgload_1.3.2.1 patchwork_1.1.2 mime_0.12
## [113] evaluate_0.21 xtable_1.8-4 smoother_1.1 fastDummies_1.6.3
## [117] IRanges_2.32.0 gridExtra_2.3 compiler_4.2.1 tibble_3.2.1
## [121] crayon_1.5.2 KernSmooth_2.23-20 htmltools_0.5.5 later_1.3.1
## [125] tidyr_1.3.0 DBI_1.1.3 tweenr_2.0.2 MASS_7.3-58.3
## [129] boot_1.3-28.1 Matrix_1.6-0 car_3.1-2 cli_3.6.1
## [133] parallel_4.2.1 dotCall64_1.0-2 igraph_1.5.0.1 GenomicRanges_1.50.2
## [137] pkgconfig_2.0.3 laeken_0.5.2 sp_2.0-0 plotly_4.10.2
## [141] spatstat.sparse_3.0-1 bslib_0.5.0 XVector_0.38.0 callr_3.7.3
## [145] stringr_1.5.0 digest_0.6.33 sctransform_0.3.5 RcppAnnoy_0.0.21
## [149] spatstat.data_3.0-1 rmarkdown_2.23 leiden_0.4.3 uwot_0.1.16
## [153] curl_5.0.1 shiny_1.7.4 ggplot.multistats_1.0.0 lifecycle_1.0.3
## [157] nlme_3.1-162 jsonlite_1.8.7 carData_3.0-5 desc_1.4.2
## [161] viridisLite_0.4.2 fansi_1.0.4 pillar_1.9.0 lattice_0.20-45
## [165] pkgbuild_1.4.0 fastmap_1.1.1 httr_1.4.6 DEoptimR_1.0-11
## [169] survival_3.5-5 remotes_2.4.2 glue_1.6.2 xts_0.13.0
## [173] png_0.1-8 profvis_0.3.7 sass_0.4.7 ggforce_0.4.1
## [177] class_7.3-21 stringi_1.7.12 RcppHNSW_0.4.1 memoise_2.0.1
## [181] dplyr_1.1.2 irlba_2.3.5.1 e1071_1.7-13 future.apply_1.11.0