mmc57bl6nj_gene_ensembl biomaRt
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Maryam • 0
@0a7b1129
Last seen 14 months ago
United States

Hi there!

I am very new to single cell RNA seq and I have been trying to get the gene ID for the mouse data that I have but I have been running into trouble with biomaRt

ensemblmart102 = useEnsembl(biomart='ENSEMBL_MART_MOUSE', dataset=' mmc57bl6nj_gene_ensembl') i have been trying to use this code but it always tells me

Error in checkDataset(dataset = dataset, mart = mart) : The given dataset: mmc57bl6nj_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function.

sessionInfo() R version 4.2.2 (2022-10-31) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Monterey 12.1

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

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] stats graphics grDevices utils
[5] datasets methods base

other attached packages: [1] biomaRt_2.54.0 BiocManager_1.30.19 [3] patchwork_1.1.2 dplyr_1.0.10
[5] SeuratObject_4.1.3 Seurat_4.3.0

loaded via a namespace (and not attached): [1] Rtsne_0.16
[2] colorspace_2.0-3
[3] deldir_1.0-6
[4] ellipsis_0.3.2
[5] ggridges_0.5.4
[6] XVector_0.38.0
[7] rstudioapi_0.14
[8] spatstat.data_3.0-0
[9] leiden_0.4.3
[10] listenv_0.9.0
[11] ggrepel_0.9.2
[12] bit64_4.0.5
[13] AnnotationDbi_1.60.0
[14] fansi_1.0.3
[15] xml2_1.3.3
[16] codetools_0.2-18
[17] splines_4.2.2
[18] cachem_1.0.6
[19] polyclip_1.10-4
[20] jsonlite_1.8.4
[21] ica_1.0-3
[22] dbplyr_2.2.1
[23] cluster_2.1.4
[24] png_0.1-8
[25] uwot_0.1.14
[26] shiny_1.7.4
[27] sctransform_0.3.5
[28] spatstat.sparse_3.0-0 [29] compiler_4.2.2
[30] httr_1.4.4
[31] assertthat_0.2.1
[32] Matrix_1.5-3
[33] fastmap_1.1.0
[34] lazyeval_0.2.2
[35] cli_3.5.0
[36] later_1.3.0
[37] prettyunits_1.1.1
[38] htmltools_0.5.4
[39] tools_4.2.2
[40] igraph_1.3.5
[41] GenomeInfoDbData_1.2.9 [42] gtable_0.3.1
[43] glue_1.6.2
[44] RANN_2.6.1
[45] reshape2_1.4.4
[46] rappdirs_0.3.3
[47] Rcpp_1.0.9
[48] Biobase_2.58.0
[49] scattermore_0.8
[50] Biostrings_2.66.0
[51] vctrs_0.5.1
[52] spatstat.explore_3.0-5 [53] nlme_3.1-161
[54] progressr_0.12.0
[55] lmtest_0.9-40
[56] spatstat.random_3.0-1 [57] stringr_1.5.0
[58] globals_0.16.2
[59] mime_0.12
[60] miniUI_0.1.1.1
[61] lifecycle_1.0.3
[62] irlba_2.3.5.1
[63] XML_3.99-0.13
[64] goftest_1.2-3
[65] future_1.30.0
[66] zlibbioc_1.44.0
[67] MASS_7.3-58.1
[68] zoo_1.8-11
[69] scales_1.2.1
[70] hms_1.1.2
[71] promises_1.2.0.1
[72] spatstat.utils_3.0-1
[73] parallel_4.2.2
[74] RColorBrewer_1.1-3
[75] curl_4.3.3
[76] memoise_2.0.1
[77] reticulate_1.26
[78] pbapply_1.6-0
[79] gridExtra_2.3
[80] ggplot2_3.4.0
[81] stringi_1.7.8
[82] RSQLite_2.2.20
[83] S4Vectors_0.36.1
[84] filelock_1.0.2
[85] BiocGenerics_0.44.0
[86] GenomeInfoDb_1.34.5
[87] bitops_1.0-7
[88] rlang_1.0.6
[89] pkgconfig_2.0.3
[90] matrixStats_0.63.0
[91] lattice_0.20-45
[92] ROCR_1.0-11
[93] purrr_1.0.0
[94] tensor_1.5
[95] htmlwidgets_1.6.0
[96] cowplot_1.1.1
[97] bit_4.0.5
[98] tidyselect_1.2.0
[99] parallelly_1.33.0
[100] RcppAnnoy_0.0.20
[101] plyr_1.8.8
[102] magrittr_2.0.3
[103] R6_2.5.1
[104] IRanges_2.32.0
[105] generics_0.1.3
[106] DBI_1.1.3
[107] withr_2.5.0
[108] pillar_1.8.1
[109] fitdistrplus_1.1-8
[110] RCurl_1.98-1.9
[111] KEGGREST_1.38.0
[112] survival_3.4-0
[113] abind_1.4-5
[114] sp_1.5-1
[115] tibble_3.1.8
[116] future.apply_1.10.0
[117] crayon_1.5.2
[118] KernSmooth_2.23-20
[119] utf8_1.2.2
[120] BiocFileCache_2.6.0
[121] spatstat.geom_3.0-3
[122] plotly_4.10.1
[123] progress_1.2.2
[124] grid_4.2.2
[125] data.table_1.14.6
[126] blob_1.2.3
[127] digest_0.6.31
[128] xtable_1.8-4
[129] tidyr_1.2.1
[130] httpuv_1.6.7
[131] stats4_4.2.2
[132] munsell_0.5.0
[133] viridisLite_0.4.1

thank you so much and I really appreciate any help

biomaRt • 711 views
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ATpoint ★ 4.0k
@atpoint-13662
Last seen 5 hours ago
Germany

There is a whitespace that needs to be removed:

enter image description here

Use: ensemblmart102 = useEnsembl(biomart='ENSEMBL_MART_MOUSE', dataset='mmc57bl6nj_gene_ensembl')

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0
Entering edit mode

I am still getting the same error for some reason

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0
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It works for me, check spelling ans typos. The code I posted is correct.

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worked!! thank you so much

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