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Dear all, I need to annotate some rnaseq data from human. I use ensemble 74. On biomart I'm not able to found? It is normal? Why?
listEnsemblArchives()
name date url
1 Ensembl GRCh37 Feb 2014 http://grch37.ensembl.org
2 Ensembl 95 Jan 2019 http://jan2019.archive.ensembl.org
3 Ensembl 94 Oct 2018 http://oct2018.archive.ensembl.org
4 Ensembl 93 Jul 2018 http://jul2018.archive.ensembl.org
5 Ensembl 92 Apr 2018 http://apr2018.archive.ensembl.org
6 Ensembl 91 Dec 2017 http://dec2017.archive.ensembl.org
7 Ensembl 90 Aug 2017 http://aug2017.archive.ensembl.org
8 Ensembl 89 May 2017 http://may2017.archive.ensembl.org
9 Ensembl 88 Mar 2017 http://mar2017.archive.ensembl.org
10 Ensembl 87 Dec 2016 http://dec2016.archive.ensembl.org
11 Ensembl 86 Oct 2016 http://oct2016.archive.ensembl.org
12 Ensembl 85 Jul 2016 http://jul2016.archive.ensembl.org
13 Ensembl 84 Mar 2016 http://mar2016.archive.ensembl.org
14 Ensembl 83 Dec 2015 http://dec2015.archive.ensembl.org
15 Ensembl 82 Sep 2015 http://sep2015.archive.ensembl.org
16 Ensembl 81 Jul 2015 http://jul2015.archive.ensembl.org
17 Ensembl 80 May 2015 http://may2015.archive.ensembl.org
18 Ensembl 79 Mar 2015 http://mar2015.archive.ensembl.org
19 Ensembl 78 Dec 2014 http://dec2014.archive.ensembl.org
20 Ensembl 77 Oct 2014 http://oct2014.archive.ensembl.org
21 Ensembl 76 Aug 2014 http://aug2014.archive.ensembl.org
22 Ensembl 75 Feb 2014 http://feb2014.archive.ensembl.org
23 Ensembl 67 May 2012 http://may2012.archive.ensembl.org
24 Ensembl 54 May 2009 http://may2009.archive.ensembl.org
version current_release
1 GRCh37
2 95 *
3 94
4 93
5 92
6 91
7 90
8 89
9 88
10 87
11 86
12 85
13 84
14 83
15 82
16 81
17 80
18 79
19 78
20 77
21 76
22 75
23 67
24 54
> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=it_IT.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=it_IT.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils
[7] datasets methods base
other attached packages:
[1] genefilter_1.64.0 limma_3.38.3
[3] biomaRt_2.38.0 reshape2_1.4.3
[5] RColorBrewer_1.1-2 ggplot2_3.1.0
[7] pheatmap_1.0.10 DESeq2_1.22.1
[9] SummarizedExperiment_1.12.0 DelayedArray_0.8.0
[11] BiocParallel_1.16.2 matrixStats_0.54.0
[13] Biobase_2.42.0 GenomicRanges_1.34.0
[15] GenomeInfoDb_1.18.1 IRanges_2.16.0
[17] S4Vectors_0.20.1 BiocGenerics_0.28.0
loaded via a namespace (and not attached):
[1] httr_1.4.0 bit64_0.9-7
[3] splines_3.5.2 Formula_1.2-3
[5] assertthat_0.2.0 latticeExtra_0.6-28
[7] blob_1.1.1 GenomeInfoDbData_1.2.0
[9] progress_1.2.0 yaml_2.2.0
[11] pillar_1.3.1 RSQLite_2.1.1
[13] backports_1.1.3 lattice_0.20-38
[15] glue_1.3.0 digest_0.6.18
[17] XVector_0.22.0 checkmate_1.8.5
[19] colorspace_1.3-2 htmltools_0.3.6
[21] Matrix_1.2-15 plyr_1.8.4
[23] XML_3.98-1.16 pkgconfig_2.0.2
[25] zlibbioc_1.28.0 purrr_0.2.5
[27] xtable_1.8-3 scales_1.0.0
[29] htmlTable_1.12 tibble_1.4.2
[31] annotate_1.60.0 withr_2.1.2
[33] nnet_7.3-12 lazyeval_0.2.1
[35] survival_2.43-3 magrittr_1.5
[37] crayon_1.3.4 memoise_1.1.0
[39] foreign_0.8-71 prettyunits_1.0.2
[41] tools_3.5.2 data.table_1.11.8
[43] hms_0.4.2 stringr_1.3.1
[45] locfit_1.5-9.1 munsell_0.5.0
[47] cluster_2.0.7-1 AnnotationDbi_1.44.0
[49] bindrcpp_0.2.2 compiler_3.5.2
[51] rlang_0.3.0.1 grid_3.5.2
[53] RCurl_1.95-4.11 rstudioapi_0.8
[55] htmlwidgets_1.3 bitops_1.0-6
[57] base64enc_0.1-3 gtable_0.2.0
[59] curl_3.2 DBI_1.0.0
[61] R6_2.3.0 gridExtra_2.3
[63] knitr_1.21 dplyr_0.7.8
[65] bit_1.1-14 bindr_0.1.1
[67] Hmisc_4.1-1 stringi_1.2.4
[69] Rcpp_1.0.0 geneplotter_1.60.0
[71] rpart_4.1-13 acepack_1.4.1
[73] tidyselect_0.2.5 xfun_0.4