egeulgen
commented
3 months ago Hey @Kur1sutaru I unfortunately couldn't replicate the issue. I'm not sure why you're getting a 403 from KEGG. This means KEGG blocked your IP address, not sure if temporarily or permanently.
If useful, there is a fairly up-to-date version of KEGG mmu gene sets (mmu_kegg_genes and mmu_kegg_descriptions) already in pathfindR.data:
> pathfindR.data_updates[grep("mmu_kegg", pathfindR.data_updates$Name),]
Category Name Description Source Version
14 Gene Sets Data mmu_kegg_genes Mus musculus KEGG Pathways - Gene Sets pathfindR:::get_kegg_gsets(org_code = "mmu") pathfindR_2.3.1.9003
15 Gene Sets Data mmu_kegg_descriptions Mus musculus KEGG Pathways - Descriptions pathfindR:::get_kegg_gsets(org_code = "mmu") pathfindR_2.3.1.9003
Last Update
14 2024-04-27
15 2024-04-27
gsets_list <- get_gene_sets_list(
R version 4.3.2 (2023-10-31) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.5
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
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/Chicago tzcode source: internal
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] pathfindR_2.3.1 pathfindR.data_2.1.0 RColorBrewer_1.1-3
[4] DEGreport_1.38.5 BiocManager_1.30.23 ggrepel_0.9.5
[7] lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1
[10] purrr_1.0.2 readr_2.1.5 tidyr_1.3.1
[13] tibble_3.2.1 tidyverse_2.0.0 pheatmap_1.0.12
[16] ggplot2_3.5.1 DESeq2_1.42.1 SummarizedExperiment_1.32.0 [19] Biobase_2.62.0 MatrixGenerics_1.14.0 matrixStats_1.3.0
[22] GenomicRanges_1.54.1 GenomeInfoDb_1.38.8 IRanges_2.36.0
[25] S4Vectors_0.40.2 BiocGenerics_0.48.1 dplyr_1.1.4
loaded via a namespace (and not attached): [1] ggdendro_0.2.0 rstudioapi_0.16.0 shape_1.4.6.1
[4] magrittr_2.0.3 farver_2.1.2 rmarkdown_2.27
[7] GlobalOptions_0.1.2 zlibbioc_1.48.2 vctrs_0.6.5
[10] memoise_2.0.1 RCurl_1.98-1.16 htmltools_0.5.8.1
[13] S4Arrays_1.2.1 curl_5.2.1 broom_1.0.6
[16] SparseArray_1.2.4 plyr_1.8.9 cachem_1.1.0
[19] igraph_2.0.3 lifecycle_1.0.4 iterators_1.0.14
[22] pkgconfig_2.0.3 Matrix_1.6-5 R6_2.5.1
[25] fastmap_1.2.0 GenomeInfoDbData_1.2.11 clue_0.3-65
[28] digest_0.6.36 colorspace_2.1-1 reshape_0.8.9
[31] labeling_0.4.3 fansi_1.0.6 timechange_0.3.0
[34] httr_1.4.7 polyclip_1.10-7 abind_1.4-5
[37] compiler_4.3.2 bit64_4.0.5 withr_3.0.0
[40] doParallel_1.0.17 ConsensusClusterPlus_1.66.0 backports_1.5.0
[43] BiocParallel_1.36.0 viridis_0.6.5 psych_2.4.6.26
[46] ggforce_0.4.2 MASS_7.3-60.0.1 DelayedArray_0.28.0
[49] rjson_0.2.21 tools_4.3.2 glue_1.7.0
[52] nlme_3.1-165 grid_4.3.2 cluster_2.1.6
[55] generics_0.1.3 hdf5r_1.3.11 gtable_0.3.5
[58] tzdb_0.4.0 hms_1.1.3 tidygraph_1.3.1
[61] utf8_1.2.4 XVector_0.42.0 foreach_1.5.2
[64] pillar_1.9.0 vroom_1.6.5 limma_3.58.1
[67] logging_0.10-108 circlize_0.4.16 tweenr_2.0.3
[70] lattice_0.22-6 bit_4.0.5 tidyselect_1.2.1
[73] ComplexHeatmap_2.18.0 locfit_1.5-9.10 Biostrings_2.70.3
[76] knitr_1.48 gridExtra_2.3 edgeR_4.0.16
[79] xfun_0.46 graphlayouts_1.1.1 statmod_1.5.0
[82] stringi_1.8.4 evaluate_0.24.0 codetools_0.2-20
[85] ggraph_2.2.1 cli_3.6.3 munsell_0.5.1
[88] Rcpp_1.0.13 png_0.1-8 parallel_4.3.2
[91] bitops_1.0-7 viridisLite_0.4.2 scales_1.3.0
[94] crayon_1.5.3 GetoptLong_1.0.5 rlang_1.1.4
[97] cowplot_1.1.3 KEGGREST_1.42.0 mnormt_2.1.1