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saezlab / dorothea

R package to access DoRothEA's regulons
https://saezlab.github.io/dorothea/
GNU General Public License v3.0
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data set 'dorothea_hs_pancancer' not found #47

Closed boseb closed 3 years ago

boseb commented 3 years ago

Hi There, TCGA regulons are not accessible. Please help.

Code: data(dorothea_hs_pancancer, package = "dorothea") Warning message: In data(dorothea_hs_pancancer, package = "dorothea") : data set 'dorothea_hs_pancancer' not found

─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────── setting value
version R version 4.0.3 (2020-10-10)
os Red Hat Enterprise Linux Server 7.5 (Maipo) system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Chicago
date 2021-08-09

christianholland commented 3 years ago

Hi @boseb,

thanks for using dorothea. Could you please let me know which version of dorothea are you using?

library(dorothea)
sessionInfo()
boseb commented 3 years ago

Hi @christianholland , I used dorothea_1.2.2

sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server 7.5 (Maipo)

Matrix products: default BLAS: /hpc/software/R/4.0.3/lib64/R/lib/libRblas.so LAPACK: /hpc/software/R/4.0.3/lib64/R/lib/libRlapack.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats4 grid splines parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0 IlluminaHumanMethylation450kmanifest_0.4.0
[3] minfi_1.36.0 dorothea_1.2.2
[5] multiMiR_1.12.0 gaston_1.5.7
[7] RcppParallel_5.1.4 Rcpp_1.0.6
[9] plyranges_1.10.0 regioneR_1.22.0
[11] BSgenome.Hsapiens.UCSC.hg38_1.4.3 BSgenome_1.58.0
[13] Biostrings_2.58.0 XVector_0.30.0
[15] biomaRt_2.46.3 BEDMatrix_2.0.3
[17] SNPRelate_1.24.0 gdsfmt_1.26.1
[19] KRIS_1.1.6 genomation_1.22.0
[21] rtracklayer_1.50.0 maftools_2.6.05
[23] sessioninfo_1.1.1 derfinderPlot_1.24.1
[25] bumphunter_1.32.0 locfit_1.5-9.4
[27] iterators_1.0.13 foreach_1.5.1
[29] GenomicState_0.99.9 AnnotationHub_2.22.1
[31] BiocFileCache_1.14.0 dbplyr_2.1.1
[33] derfinder_1.24.2 gplots_3.1.1
[35] org.Hs.eg.db_3.12.0 AnnotationDbi_1.52.0
[37] clusterProfiler_3.18.1 regionReport_1.24.2
[39] DESeq2_1.30.1 edgeR_3.32.1
[41] limma_3.46.0 recount_1.16.1
[43] TCGAbiolinks_2.18.0 SummarizedExperiment_1.20.0
[45] Biobase_2.50.0 GenomicRanges_1.42.0
[47] GenomeInfoDb_1.26.7 IRanges_2.24.1
[49] S4Vectors_0.28.1 BiocGenerics_0.36.1
[51] MatrixGenerics_1.2.1 matrixStats_0.59.0
[53] rlang_0.4.11 forcats_0.5.1
[55] dplyr_1.0.6 purrr_0.3.4
[57] tibble_3.1.2 ggplot2_3.3.5
[59] tidyverse_1.3.1 vctrs_0.3.8
[61] tidyr_1.1.3 matrixcalc_1.0-4
[63] PMA_1.2.1 CCA_1.2.1
[65] fields_12.3 viridis_0.6.1
[67] viridisLite_0.4.0 spam_2.6-0
[69] dotCall64_1.0-1 fda_5.1.9
[71] fds_1.8 RCurl_1.98-1.3
[73] rainbow_3.6 pcaPP_1.9-74
[75] MASS_7.3-53 Matrix_1.3-4
[77] readr_1.4.0 plyr_1.8.6
[79] janitor_2.1.0 reshape2_1.4.4
[81] reshape_0.8.8 sqldf_0.4-11
[83] RSQLite_2.2.7 gsubfn_0.7
[85] proto_1.0.0 data.table_1.14.0
[87] stringr_1.4.0 statmod_1.4.36

loaded via a namespace (and not attached): [1] Hmisc_4.5-0 Rsamtools_2.6.0 crayon_1.4.1
[4] rhdf5filters_1.2.1 nlme_3.1-149 backports_1.2.1
[7] reprex_2.0.0 impute_1.64.0 GOSemSim_2.16.1
[10] readxl_1.3.1 BiocParallel_1.24.1 bcellViper_1.26.0
[13] bit64_4.0.5 glue_1.4.2 rngtools_1.5
[16] DEFormats_1.18.0 tcltk_4.0.3 DOSE_3.16.0
[19] haven_2.4.1 tidyselect_1.1.1 XML_3.99-0.6
[22] GenomicAlignments_1.26.0 chron_2.3-56 xtable_1.8-4
[25] magrittr_2.0.1 evaluate_0.14 cli_2.5.0
[28] zlibbioc_1.36.0 rstudioapi_0.13 doRNG_1.8.2
[31] rpart_4.1-15 fastmatch_1.1-0 derfinderHelper_1.24.1
[34] BiocStyle_2.18.1 ensembldb_2.14.1 seqPattern_1.22.0
[37] maps_3.3.0 shiny_1.6.0 xfun_0.23
[40] askpass_1.1 multtest_2.46.0 cluster_2.1.0
[43] caTools_1.18.2 tidygraph_1.2.0 interactiveDisplayBase_1.28.0 [46] base64_2.0 ggrepel_0.9.1 scrime_1.3.5
[49] biovizBase_1.38.0 png_0.1-7 withr_2.4.2
[52] bitops_1.0-7 ggforce_0.3.3 RBGL_1.66.0
[55] cellranger_1.1.0 AnnotationFilter_1.14.0 pracma_2.3.3
[58] pillar_1.6.1 cachem_1.0.5 GenomicFeatures_1.42.3
[61] fs_1.5.0 DelayedMatrixStats_1.12.3 ellipsis_0.3.2
[64] generics_0.1.0 tools_4.0.3 foreign_0.8-80
[67] munsell_0.5.0 tweenr_1.0.2 fgsea_1.16.0
[70] DelayedArray_0.16.3 fastmap_1.1.0 compiler_4.0.3
[73] httpuv_1.6.1 beanplot_1.2 GenomeInfoDbData_1.2.4
[76] gridExtra_2.3 lattice_0.20-41 utf8_1.2.1
[79] later_1.2.0 jsonlite_1.7.2 GGally_2.1.2
[82] scales_1.1.1 graph_1.68.0 sparseMatrixStats_1.2.1
[85] genefilter_1.72.1 lazyeval_0.2.2 promises_1.2.0.1
[88] latticeExtra_0.6-29 R.utils_2.10.1 checkmate_2.0.0
[91] nor1mix_1.3-0 rmarkdown_2.8 cowplot_1.1.1
[94] rARPACK_0.11-0 siggenes_1.64.0 crochet_2.3.0
[97] dichromat_2.0-0 downloader_0.4 igraph_1.2.6
[100] HDF5Array_1.18.1 survival_3.2-7 yaml_2.2.1
[103] plotrix_3.8-1 htmltools_0.5.1.1 memoise_2.0.0
[106] VariantAnnotation_1.36.0 quadprog_1.5-8 graphlayouts_0.7.1
[109] digest_0.6.27 assertthat_0.2.1 mime_0.10
[112] rappdirs_0.3.3 knitrBootstrap_1.0.2 TCGAbiolinksGUI.data_1.10.0
[115] blob_1.2.1 R.oo_1.24.0 preprocessCore_1.52.1
[118] Formula_1.2-4 Rhdf5lib_1.12.1 illuminaio_0.32.0
[121] OrganismDbi_1.32.0 ProtGenerics_1.22.0 broom_0.7.6
[124] ks_1.13.1 hms_1.1.0 modelr_0.1.8
[127] rhdf5_2.34.0 colorspace_2.0-1 base64enc_0.1-3
[130] BiocManager_1.30.15 nnet_7.3-14 GEOquery_2.58.0
[133] mclust_5.4.7 mvtnorm_1.1-2 enrichplot_1.10.2
[136] fansi_0.5.0 R6_2.5.0 lifecycle_1.0.0
[139] curl_4.3.1 snakecase_0.11.0 DO.db_2.9
[142] qvalue_2.22.0 ggbio_1.38.0 RColorBrewer_1.1-2
[145] RefManageR_1.3.0 htmlwidgets_1.5.3 polyclip_1.10-0
[148] markdown_1.1 shadowtext_0.0.8 rvest_1.0.0
[151] openssl_1.4.4 htmlTable_2.2.1 codetools_0.2-16
[154] lubridate_1.7.10 GO.db_3.12.1 gtools_3.9.2
[157] prettyunits_1.1.1 gridBase_0.4-7 RSpectra_0.16-0
[160] R.methodsS3_1.8.1 gtable_0.3.0 DBI_1.1.1
[163] httr_1.4.2 KernSmooth_2.23-17 stringi_1.6.2
[166] progress_1.2.2 farver_2.1.0 annotate_1.68.0
[169] rentrez_1.2.3 xml2_1.3.2 rvcheck_0.1.8
[172] geneplotter_1.68.0 BiocVersion_3.12.0 bit_4.0.4
[175] scatterpie_0.1.6 jpeg_0.1-8.1 ggraph_2.0.5
[178] pkgconfig_2.0.3 knitr_1.33 GenomicFiles_1.26.0
[181] hdrcde_3.4

christianholland commented 3 years ago

Please install the latest version (1.4.1) from Bioconductor to have access to the pancancer regulons