Question: Homo.sapiens - hg38 build?
1
gravatar for bsmith030465
2.4 years ago by
bsmith030465110
United States
bsmith030465110 wrote:

Hi,

I downloaded and installed the package "Homo.sapiens" but when I load it, I see that it's based on hg19. Is there a version based on the more recent hg38?

thanks!

======================

My command and sessionInfo:

library(Homo.sapiens) Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply,
parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

IQR, mad, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq, Filter,
Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff,
sort, table, tapply, union, unique, unsplit

Loading required package: Biobase Welcome to Bioconductor

Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: OrganismDbi Loading required package: GenomicFeatures Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: GO.db

Loading required package: org.Hs.eg.db

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene

sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.4 (El Capitan)

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] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] Homo.sapiens_1.3.1 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 [3] org.Hs.eg.db_3.3.0 GO.db_3.3.0
[5] OrganismDbi_1.14.1 GenomicFeatures_1.24.5
[7] GenomicRanges_1.24.2 GenomeInfoDb_1.8.3
[9] AnnotationDbi_1.34.4 IRanges_2.6.1
[11] S4Vectors_0.10.2 Biobase_2.32.0
[13] BiocGenerics_0.18.0 BiocInstaller_1.22.3

loaded via a namespace (and not attached): [1] graph_1.50.0 XVector_0.12.1 zlibbioc_1.18.0 GenomicAlignments_1.8.4
[5] BiocParallel_1.6.3 tools_3.3.1 SummarizedExperiment_1.2.3 DBI_0.4-1
[9] RBGL_1.48.1 rtracklayer_1.32.2 bitops_1.0-6 RCurl_1.95-4.8
[13] biomaRt_2.28.0 RSQLite_1.0.0 Biostrings_2.40.2 Rsamtools_1.24.0
[17] XML_3.98-1.4

organismdbi homo.sapiens • 1.5k views
ADD COMMENTlink modified 2.4 years ago by WouterDeCoster35k • written 2.4 years ago by bsmith030465110
0
gravatar for WouterDeCoster
2.4 years ago by
Belgium
WouterDeCoster35k wrote:

Based on http://bioconductor.org/packages/release/bioc/vignettes/OrganismDbi/inst/doc/OrganismDbi.pdf Homo.sapiens seems exclusively hg19. Depending on what you want to do, https://github.com/stephenturner/annotables might be an alternative.

ADD COMMENTlink written 2.4 years ago by WouterDeCoster35k
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