Entering edit mode
Hello, it looks like org.Rn,eg.db
(and others like it) are not yet available for R version 3.3.3:
> biocLite("org.Rn,eg.db") BioC_mirror: https://bioconductor.org Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.3 (2017-03-06). Installing package(s) ‘org.Rn,eg.db’ Warning message: package ‘org.Rn,eg.db’ is not available (for R version 3.3.3)
Here is my sessionInfo()
for reference:
> sessionInfo() R version 3.3.3 (2017-03-06) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X Yosemite 10.10.5 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] splines stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] GEOmetadb_1.32.2 RSQLite_2.0 GEOquery_2.38.4 [4] geneXtendeR_1.0.2 data.table_1.10.4 mygene_1.8.0 [7] GenomicFeatures_1.24.5 AnnotationDbi_1.34.4 DEGseq_1.26.0 [10] samr_2.0 matrixStats_0.52.2 impute_1.46.0 [13] qvalue_2.4.2 PoissonSeq_1.1.2 combinat_0.0-8 [16] BiocInstaller_1.22.3 baySeq_2.6.0 perm_1.0-0.0 [19] abind_1.4-5 EBSeq_1.12.0 testthat_1.0.2 [22] blockmodeling_0.1.9 DESeq2_1.12.4 SummarizedExperiment_1.2.3 [25] Biobase_2.32.0 edgeR_3.14.0 limma_3.28.21 [28] dplyr_0.7.1 gplots_3.0.1 shinyapps_0.4.1.8 [31] shiny_1.0.3 bindrcpp_0.2 rtracklayer_1.32.2 [34] GenomicRanges_1.24.3 GenomeInfoDb_1.8.7 IRanges_2.6.1 [37] S4Vectors_0.10.3 BiocGenerics_0.18.0 devtools_1.13.2 loaded via a namespace (and not attached): [1] backports_1.1.0 Hmisc_4.0-3 plyr_1.8.4 lazyeval_0.2.0 [5] BiocParallel_1.6.6 ggplot2_2.2.1 digest_0.6.12 htmltools_0.3.6 [9] gdata_2.18.0 magrittr_1.5 checkmate_1.8.3 memoise_1.1.0 [13] cluster_2.0.6 Biostrings_2.40.2 annotate_1.50.1 colorspace_1.3-2 [17] blob_1.1.0 crayon_1.3.2 RCurl_1.95-4.8 jsonlite_1.5 [21] roxygen2_6.0.1 genefilter_1.54.2 bindr_0.1 survival_2.41-3 [25] glue_1.1.1 gtable_0.2.0 zlibbioc_1.18.0 XVector_0.12.1 [29] scales_0.4.1 DBI_0.7 Rcpp_0.12.11 xtable_1.8-2 [33] htmlTable_1.9 foreign_0.8-69 bit_1.1-12 Formula_1.2-2 [37] sqldf_0.4-11 htmlwidgets_0.9 httr_1.2.1 RColorBrewer_1.1-2 [41] acepack_1.4.1 pkgconfig_2.0.1 XML_3.98-1.9 nnet_7.3-12 [45] locfit_1.5-9.1 rlang_0.1.1 reshape2_1.4.2 munsell_0.4.3 [49] tools_3.3.3 gsubfn_0.6-6 stringr_1.2.0 knitr_1.16 [53] bit64_0.9-7 caTools_1.17.1 mime_0.5 xml2_1.1.1 [57] biomaRt_2.28.0 curl_2.7 tibble_1.3.3 geneplotter_1.50.0 [61] stringi_1.1.5 desc_1.1.0 lattice_0.20-35 Matrix_1.2-10 [65] commonmark_1.2 bitops_1.0-6 httpuv_1.3.5 R6_2.2.2 [69] latticeExtra_0.6-28 KernSmooth_2.23-15 gridExtra_2.2.1 gtools_3.5.0 [73] assertthat_0.2.0.9000 chron_2.3-50 proto_1.0.0 rprojroot_1.2 [77] withr_1.0.2 GenomicAlignments_1.8.4 Rsamtools_1.24.0 grid_3.3.3 [81] rpart_4.1-11 git2r_0.18.0 base64enc_0.1-3
Oops, didn't notice the comma in: A: Returning gene functional annotations with gene symbols as input (using mygene B. Thanks for the catch!