Hi,
I try to use progeny for mouse, but I have an error message.
net <- get_progeny(organism = 'mouse', top = 500)
[2024-12-27 18:04:06] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2024-12-27 18:04:07] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 2 records
Error in UseMethod("rename") :
no applicable method for 'rename' applied to an object of class "list"_
`sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-apple-darwin20
Running under: macOS Sonoma 14.6.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] pheatmap_1.0.12 patchwork_1.3.0 tidyr_1.3.1 tibble_3.2.1
[5] viper_1.38.0 Biobase_2.64.0 BiocGenerics_0.50.0 OmnipathR_3.12.4
[9] decoupleR_2.10.0 scCustomize_3.0.1 ggbeeswarm_0.7.2 RColorBrewer_1.1-3
[13] wesanderson_0.3.7 viridis_0.6.5 viridisLite_0.4.2 ggplot2_3.5.1
[17] stringr_1.5.1 dplyr_1.1.4 Seurat_5.1.0 SeuratObject_5.0.2
[21] sp_2.1-4
loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.22 splines_4.4.2 later_1.4.1
[4] cellranger_1.1.0 polyclip_1.10-7 janitor_2.2.1
[7] fastDummies_1.7.4 lifecycle_1.0.4 globals_0.16.3
[10] lattice_0.22-6 vroom_1.6.5 MASS_7.3-61
[13] backports_1.5.0 magrittr_2.0.3 plotly_4.10.4
[16] rmarkdown_2.29 yaml_2.3.10 httpuv_1.6.15
[19] sctransform_0.4.1 spam_2.11-0 spatstat.sparse_3.1-0
[22] reticulate_1.40.0 cowplot_1.1.3 pbapply_1.7-2
[25] lubridate_1.9.4 abind_1.4-8 rvest_1.0.4
[28] Rtsne_0.17 mixtools_2.0.0 purrr_1.0.2
[31] rappdirs_0.3.3 circlize_0.4.16 ggrepel_0.9.6
[34] irlba_2.3.5.1 listenv_0.9.1 spatstat.utils_3.1-1
[37] goftest_1.2-3 RSpectra_0.16-2 spatstat.random_3.3-2
[40] fitdistrplus_1.2-1 parallelly_1.41.0 leiden_0.4.3.1
[43] codetools_0.2-20 xml2_1.3.6 tidyselect_1.2.1
[46] shape_1.4.6.1 farver_2.1.2 matrixStats_1.4.1
[49] spatstat.explore_3.3-3 jsonlite_1.8.9 e1071_1.7-16
[52] progressr_0.15.1 ggridges_0.5.6 survival_3.8-3
[55] segmented_2.1-3 tools_4.4.2 progress_1.2.3
[58] ica_1.0-3 Rcpp_1.0.13-1 glue_1.8.0
[61] gridExtra_2.3 xfun_0.49 withr_3.0.2
[64] BiocManager_1.30.25 fastmap_1.2.0 digest_0.6.37
[67] timechange_0.3.0 R6_2.5.1 mime_0.12
[70] ggprism_1.0.5 colorspace_2.1-1 scattermore_1.2
[73] tensor_1.5 spatstat.data_3.1-4 utf8_1.2.4
[76] generics_0.1.3 data.table_1.16.4 class_7.3-22
[79] prettyunits_1.2.0 httr_1.4.7 htmlwidgets_1.6.4
[82] uwot_0.2.2 pkgconfig_2.0.3 gtable_0.3.6
[85] lmtest_0.9-40 selectr_0.4-2 htmltools_0.5.8.1
[88] dotCall64_1.2 scales_1.3.0 png_0.1-8
[91] spatstat.univar_3.1-1 snakecase_0.11.1 knitr_1.49
[94] rstudioapi_0.17.1 tzdb_0.4.0 reshape2_1.4.4
[97] checkmate_2.3.2 nlme_3.1-166 curl_6.0.1
[100] proxy_0.4-27 zoo_1.8-12 GlobalOptions_0.1.2
[103] KernSmooth_2.23-24 parallel_4.4.2 miniUI_0.1.1.1
[106] vipor_0.4.7 ggrastr_1.0.2 pillar_1.10.0
[109] grid_4.4.2 logger_0.4.0 vctrs_0.6.5
[112] RANN_2.6.2 promises_1.3.2 xtable_1.8-4
[115] cluster_2.1.8 beeswarm_0.4.0 paletteer_1.6.0
[118] evaluate_1.0.1 readr_2.1.5 cli_3.6.3
[121] compiler_4.4.2 rlang_1.1.4 crayon_1.5.3
[124] future.apply_1.11.3 labeling_0.4.3 rematch2_2.1.2
[127] plyr_1.8.9 forcats_1.0.0 stringi_1.8.4
[130] deldir_2.0-4 BiocParallel_1.38.0 munsell_0.5.1
[133] lazyeval_0.2.2 spatstat.geom_3.3-4 Matrix_1.7-1
[136] RcppHNSW_0.6.0 hms_1.1.3 bit64_4.5.2
[139] future_1.34.0 shiny_1.10.0 kernlab_0.9-33
[142] ROCR_1.0-11 igraph_2.1.2 bit_4.5.0.1
[145] readxl_1.4.3 `
Hi,
I try to use progeny for mouse, but I have an error message.
net <- get_progeny(organism = 'mouse', top = 500)[2024-12-27 18:04:06] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2024-12-27 18:04:07] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 2 records
Error in UseMethod("rename") :
no applicable method for 'rename' applied to an object of class "list"_
`sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-apple-darwin20
Running under: macOS Sonoma 14.6.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] pheatmap_1.0.12 patchwork_1.3.0 tidyr_1.3.1 tibble_3.2.1
[5] viper_1.38.0 Biobase_2.64.0 BiocGenerics_0.50.0 OmnipathR_3.12.4
[9] decoupleR_2.10.0 scCustomize_3.0.1 ggbeeswarm_0.7.2 RColorBrewer_1.1-3
[13] wesanderson_0.3.7 viridis_0.6.5 viridisLite_0.4.2 ggplot2_3.5.1
[17] stringr_1.5.1 dplyr_1.1.4 Seurat_5.1.0 SeuratObject_5.0.2
[21] sp_2.1-4
loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.22 splines_4.4.2 later_1.4.1
[4] cellranger_1.1.0 polyclip_1.10-7 janitor_2.2.1
[7] fastDummies_1.7.4 lifecycle_1.0.4 globals_0.16.3
[10] lattice_0.22-6 vroom_1.6.5 MASS_7.3-61
[13] backports_1.5.0 magrittr_2.0.3 plotly_4.10.4
[16] rmarkdown_2.29 yaml_2.3.10 httpuv_1.6.15
[19] sctransform_0.4.1 spam_2.11-0 spatstat.sparse_3.1-0
[22] reticulate_1.40.0 cowplot_1.1.3 pbapply_1.7-2
[25] lubridate_1.9.4 abind_1.4-8 rvest_1.0.4
[28] Rtsne_0.17 mixtools_2.0.0 purrr_1.0.2
[31] rappdirs_0.3.3 circlize_0.4.16 ggrepel_0.9.6
[34] irlba_2.3.5.1 listenv_0.9.1 spatstat.utils_3.1-1
[37] goftest_1.2-3 RSpectra_0.16-2 spatstat.random_3.3-2
[40] fitdistrplus_1.2-1 parallelly_1.41.0 leiden_0.4.3.1
[43] codetools_0.2-20 xml2_1.3.6 tidyselect_1.2.1
[46] shape_1.4.6.1 farver_2.1.2 matrixStats_1.4.1
[49] spatstat.explore_3.3-3 jsonlite_1.8.9 e1071_1.7-16
[52] progressr_0.15.1 ggridges_0.5.6 survival_3.8-3
[55] segmented_2.1-3 tools_4.4.2 progress_1.2.3
[58] ica_1.0-3 Rcpp_1.0.13-1 glue_1.8.0
[61] gridExtra_2.3 xfun_0.49 withr_3.0.2
[64] BiocManager_1.30.25 fastmap_1.2.0 digest_0.6.37
[67] timechange_0.3.0 R6_2.5.1 mime_0.12
[70] ggprism_1.0.5 colorspace_2.1-1 scattermore_1.2
[73] tensor_1.5 spatstat.data_3.1-4 utf8_1.2.4
[76] generics_0.1.3 data.table_1.16.4 class_7.3-22
[79] prettyunits_1.2.0 httr_1.4.7 htmlwidgets_1.6.4
[82] uwot_0.2.2 pkgconfig_2.0.3 gtable_0.3.6
[85] lmtest_0.9-40 selectr_0.4-2 htmltools_0.5.8.1
[88] dotCall64_1.2 scales_1.3.0 png_0.1-8
[91] spatstat.univar_3.1-1 snakecase_0.11.1 knitr_1.49
[94] rstudioapi_0.17.1 tzdb_0.4.0 reshape2_1.4.4
[97] checkmate_2.3.2 nlme_3.1-166 curl_6.0.1
[100] proxy_0.4-27 zoo_1.8-12 GlobalOptions_0.1.2
[103] KernSmooth_2.23-24 parallel_4.4.2 miniUI_0.1.1.1
[106] vipor_0.4.7 ggrastr_1.0.2 pillar_1.10.0
[109] grid_4.4.2 logger_0.4.0 vctrs_0.6.5
[112] RANN_2.6.2 promises_1.3.2 xtable_1.8-4
[115] cluster_2.1.8 beeswarm_0.4.0 paletteer_1.6.0
[118] evaluate_1.0.1 readr_2.1.5 cli_3.6.3
[121] compiler_4.4.2 rlang_1.1.4 crayon_1.5.3
[124] future.apply_1.11.3 labeling_0.4.3 rematch2_2.1.2
[127] plyr_1.8.9 forcats_1.0.0 stringi_1.8.4
[130] deldir_2.0-4 BiocParallel_1.38.0 munsell_0.5.1
[133] lazyeval_0.2.2 spatstat.geom_3.3-4 Matrix_1.7-1
[136] RcppHNSW_0.6.0 hms_1.1.3 bit64_4.5.2
[139] future_1.34.0 shiny_1.10.0 kernlab_0.9-33
[142] ROCR_1.0-11 igraph_2.1.2 bit_4.5.0.1
[145] readxl_1.4.3 `