Entering edit mode
Hello,
I'm trying to use the 'cgpicr_gene_ensembl' dataset in biomart and tried exactly as in this post:
Convert mouse gene ids to hamster gene ids
but the dataset is missing ?
> datasets <- listDatasets(useMart('ensembl'))
> datasets[grep('Chinese', datasets[,2]),]
dataset description version
29 cgchok1gshd_gene_ensembl Chinese hamster CHOK1GS genes (CHOK1GS_HDv1) CHOK1GS_HDv1
136 osinensis_gene_ensembl Chinese medaka genes (ASM858656v1) ASM858656v1
158 psinensis_gene_ensembl Chinese softshell turtle genes (PelSin_1.0) PelSin_1.0
sessionInfo( )
R version 4.1.3 (2022-03-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.50.3 tidyr_1.2.0
loaded via a namespace (and not attached):
[1] KEGGREST_1.34.0 progress_1.2.2 tidyselect_1.1.2 purrr_0.3.4 vctrs_0.3.8
[6] generics_0.1.2 stats4_4.1.3 BiocFileCache_2.2.1 utf8_1.2.2 blob_1.2.2
[11] XML_3.99-0.9 rlang_1.0.2 pillar_1.7.0 withr_2.5.0 glue_1.6.2
[16] DBI_1.1.2 rappdirs_0.3.3 BiocGenerics_0.40.0 bit64_4.0.5 dbplyr_2.1.1
[21] GenomeInfoDbData_1.2.7 lifecycle_1.0.1 stringr_1.4.0 zlibbioc_1.40.0 Biostrings_2.62.0
[26] memoise_2.0.1 Biobase_2.54.0 IRanges_2.28.0 fastmap_1.1.0 GenomeInfoDb_1.30.1
[31] curl_4.3.2 AnnotationDbi_1.56.2 fansi_1.0.3 Rcpp_1.0.8.3 filelock_1.0.2
[36] BiocManager_1.30.16 cachem_1.0.6 S4Vectors_0.32.3 XVector_0.34.0 bit_4.0.4
[41] hms_1.1.1 png_0.1-7 digest_0.6.29 stringi_1.7.6 dplyr_1.0.8
[46] cli_3.2.0 tools_4.1.3 bitops_1.0-7 magrittr_2.0.2 RCurl_1.98-1.6
[51] tibble_3.1.6 RSQLite_2.2.11 crayon_1.5.0 pkgconfig_2.0.3 ellipsis_0.3.2
[56] xml2_1.3.3 prettyunits_1.1.1 assertthat_0.2.1 httr_1.4.2 R6_2.5.1
[61] compiler_4.1.3
