Entering edit mode
Hi,
I am using MAGeCKFlute to analyze my summary file from MAGeCK.
However, when I run
path.geneSummary <- "./Gr1PosvsGr1Neg.Ivo.gene_summary.txt"
path.sgRNASummary <- "./Gr1PosvsGr1Neg.Ivo.sgrna_summary.txt"
FluteRRA(gene_summary = path.geneSummary,
sgrna_summary = path.sgRNASummary,
proj = "Apr08",
organism = "mmu"
)
It throws the error
Error in bmRequest(request = request, verbose = verbose) :
Internal Server Error (HTTP 500).
When I run the function EnrichAnalyzer, it also creates the same error.
enrich <- EnrichAnalyzer(genelist, method = "GSEA", type = "GOBP")
2020-04-08 20:15:27 # Running GOBP enrichment analysis
2020-Apr-08 8:15:27 PM Downloading genesets from Gene Ontology ...
Error in bmRequest(request = request, verbose = verbose) :
Internal Server Error (HTTP 500).
md5-6402c169a4e26d9f981ca377fced1997
sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_Canada.1252
[2] LC_CTYPE=English_Canada.1252
[3] LC_MONETARY=English_Canada.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_Canada.1252
attached base packages:
[1] stats graphics grDevices utils datasets
[6] methods base
other attached packages:
[1] forcats_0.5.0 stringr_1.4.0 dplyr_0.8.5
[4] purrr_0.3.3 readr_1.3.1 tidyr_1.0.2
[7] tibble_2.1.3 ggplot2_3.3.0 tidyverse_1.3.0
[10] MAGeCKFlute_1.6.3
loaded via a namespace (and not attached):
[1] readxl_1.3.1 backports_1.1.5
[3] fastmatch_1.1-0 BiocFileCache_1.10.2
[5] plyr_1.8.6 igraph_1.2.4.2
[7] splines_3.6.2 BiocParallel_1.20.1
[9] pathview_1.26.0 sva_3.34.0
[11] urltools_1.7.3 digest_0.6.25
[13] GOSemSim_2.12.1 viridis_0.5.1
[15] GO.db_3.10.0 fansi_0.4.1
[17] magrittr_1.5 memoise_1.1.0
[19] limma_3.42.2 Biostrings_2.54.0
[21] annotate_1.64.0 graphlayouts_0.6.0
[23] modelr_0.1.6 matrixStats_0.56.0
[25] askpass_1.1 enrichplot_1.6.1
[27] prettyunits_1.1.1 colorspace_1.4-1
[29] rvest_0.3.5 blob_1.2.1
[31] rappdirs_0.3.1 ggrepel_0.8.2
[33] haven_2.2.0 xfun_0.12
[35] crayon_1.3.4 RCurl_1.98-1.1
[37] jsonlite_1.6.1 graph_1.64.0
[39] genefilter_1.68.0 survival_3.1-8
[41] glue_1.3.2 polyclip_1.10-0
[43] gtable_0.3.0 zlibbioc_1.32.0
[45] XVector_0.26.0 Rgraphviz_2.30.0
[47] BiocGenerics_0.32.0 scales_1.1.0
[49] DOSE_3.12.0 pheatmap_1.0.12
[51] DBI_1.1.0 Rcpp_1.0.4
[53] viridisLite_0.3.0 xtable_1.8-4
[55] progress_1.2.2 gridGraphics_0.5-0
[57] bit_1.1-15.2 europepmc_0.3
[59] stats4_3.6.2 httr_1.4.1
[61] fgsea_1.12.0 RColorBrewer_1.1-2
[63] pkgconfig_2.0.3 XML_3.99-0.3
[65] farver_2.0.3 dbplyr_1.4.2
[67] ggplotify_0.0.5 tidyselect_1.0.0
[69] labeling_0.3 rlang_0.4.5
[71] reshape2_1.4.3 AnnotationDbi_1.48.0
[73] munsell_0.5.0 cellranger_1.1.0
[75] tools_3.6.2 cli_2.0.2
[77] generics_0.0.2 RSQLite_2.2.0
[79] broom_0.5.5 ggridges_0.5.2
[81] yaml_2.2.1 fs_1.3.2
[83] knitr_1.28 bit64_0.9-7
[85] tidygraph_1.1.2 KEGGREST_1.26.1
[87] dendextend_1.13.4 ggraph_2.0.1
[89] nlme_3.1-142 KEGGgraph_1.46.0
[91] DO.db_2.9 xml2_1.2.5
[93] biomaRt_2.42.0 compiler_3.6.2
[95] rstudioapi_0.11 curl_4.3
[97] png_0.1-7 ggsignif_0.6.0
[99] reprex_0.3.0 tweenr_1.0.1
[101] stringi_1.4.6 lattice_0.20-38
[103] Matrix_1.2-18 ggsci_2.9
[105] vctrs_0.2.4 pillar_1.4.3
[107] lifecycle_0.2.0 BiocManager_1.30.10
[109] triebeard_0.3.0 data.table_1.12.8
[111] cowplot_1.0.0 bitops_1.0-6
[113] qvalue_2.18.0 R6_2.4.1
[115] gridExtra_2.3 IRanges_2.20.2
[117] MASS_7.3-51.5 assertthat_0.2.1
[119] openssl_1.4.1 withr_2.1.2
[121] S4Vectors_0.24.3 mgcv_1.8-31
[123] parallel_3.6.2 hms_0.5.3
[125] clusterProfiler_3.14.3 grid_3.6.2
[127] rvcheck_0.1.8 ggpubr_0.2.5
[129] ggforce_0.3.1 Biobase_2.46.0
[131] lubridate_1.7.4
