rGenomeTracksData is a collection of sample genomic and epigenomic data for demonstrating rGenomeTracks package.
This data is provided by pyGenomeTracks project.
| Name | Type |
|---|---|
| bigwig2_X_2.5e6_3.5e6.bw | bigwig |
| dm3_genes.bed.gz" | bed12 |
| dm3_genes.bed4.gz" | bed4 |
| dm3_genes.bed6.gz" | bed6 |
| dm3_subset_BDGP5.78.gtf.gz" | gtf |
| epilog.qcat.bgz" | qcat |
| GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" | bedGraph |
| HoxD_cluster_regulatory_regions_mm10.bed" | bed |
| Li_et_al_2015.cool | HDF5 compressed sparse (cool) |
| Li_et_al_2015.h5 | HDF5 |
| links2.links | bed links |
| tad_classification.bed | bed |
| test.arcs | bed links |
| test2.narrowPeak | narrowPeak |
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ObMiTi")# loading required libraries
library(rGenomeTracksData)
#> Loading required package: AnnotationHub
#> Loading required package: BiocGenerics
#>
#> Attaching package: 'BiocGenerics'
#> The following objects are masked from 'package:stats':
#>
#> IQR, mad, sd, var, xtabs
#> The following objects are masked from 'package:base':
#>
#> Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#> as.data.frame, basename, cbind, colnames, dirname, do.call,
#> duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
#> lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
#> pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
#> tapply, union, unique, unsplit, which.max, which.min
#> Loading required package: BiocFileCache
#> Loading required package: dbplyr
library(AnnotationHub)ah <- AnnotationHub()
#> snapshotDate(): 2021-09-10
query(ah, "rGenomeTracksData")
#> AnnotationHub with 16 records
#> # snapshotDate(): 2021-09-10
#> # $dataprovider: pyGenomeTracks
#> # $species: Drosophila melanogaster, Mus musculus
#> # $rdataclass: String
#> # additional mcols(): taxonomyid, genome, description,
#> # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#> # rdatapath, sourceurl, sourcetype
#> # retrieve records with, e.g., 'object[["AH95890"]]'
#>
#> title
#> AH95890 | bedgraph_chrx_2e6_5e6.bg.bgz
#> AH95891 | bigwig2_X_2.5e6_3.5e6.bw
#> AH95892 | chromatinStates_kc.bed.gz
#> AH95893 | dm3_genes.bed.gz
#> AH95894 | dm3_genes.bed4.gz
#> ... ...
#> AH95901 | Li_et_al_2015.h5
#> AH95902 | links2.links
#> AH95903 | tad_classification.bed
#> AH95904 | test.arcs
#> AH95905 | test2.narrowPeakAfter saving the query object, you can access the file you want like that:
# locate the file you want for loading from the track
bigwig_file <- ah[["AH95891"]]
#> downloading 1 resources
#> retrieving 1 resource
#> loading from cacheThe object is a path to the local directory to the downloaded file.
sessionInfo()
#> R version 4.1.1 Patched (2021-09-10 r80880)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 18.04.5 LTS
#>
#> Matrix products: default
#> BLAS: /home/shepherd/R-Installs/bin/R-4-1-branch/lib/libRblas.so
#> LAPACK: /home/shepherd/R-Installs/bin/R-4-1-branch/lib/libRlapack.so
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
#> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] rGenomeTracksData_0.99.0 AnnotationHub_3.1.5 BiocFileCache_2.1.1
#> [4] dbplyr_2.1.1 BiocGenerics_0.39.2
#>
#> loaded via a namespace (and not attached):
#> [1] Rcpp_1.0.7 png_0.1-7
#> [3] Biostrings_2.61.2 assertthat_0.2.1
#> [5] digest_0.6.27 utf8_1.2.2
#> [7] mime_0.11 R6_2.5.1
#> [9] GenomeInfoDb_1.29.8 stats4_4.1.1
#> [11] RSQLite_2.2.8 evaluate_0.14
#> [13] httr_1.4.2 pillar_1.6.2
#> [15] zlibbioc_1.39.0 rlang_0.4.11
#> [17] curl_4.3.2 jquerylib_0.1.4
#> [19] blob_1.2.2 S4Vectors_0.31.3
#> [21] rmarkdown_2.11 stringr_1.4.0
#> [23] RCurl_1.98-1.5 bit_4.0.4
#> [25] shiny_1.7.0 compiler_4.1.1
#> [27] httpuv_1.6.3 xfun_0.26
#> [29] pkgconfig_2.0.3 htmltools_0.5.2
#> [31] tidyselect_1.1.1 KEGGREST_1.33.0
#> [33] tibble_3.1.4 GenomeInfoDbData_1.2.6
#> [35] interactiveDisplayBase_1.31.2 IRanges_2.27.2
#> [37] fansi_0.5.0 withr_2.4.2
#> [39] crayon_1.4.1 dplyr_1.0.7
#> [41] later_1.3.0 bitops_1.0-7
#> [43] rappdirs_0.3.3 jsonlite_1.7.2
#> [45] xtable_1.8-4 lifecycle_1.0.0
#> [47] DBI_1.1.1 magrittr_2.0.1
#> [49] stringi_1.7.4 cachem_1.0.6
#> [51] XVector_0.33.0 promises_1.2.0.1
#> [53] bslib_0.3.0 ellipsis_0.3.2
#> [55] filelock_1.0.2 generics_0.1.0
#> [57] vctrs_0.3.8 tools_4.1.1
#> [59] bit64_4.0.5 Biobase_2.53.0
#> [61] glue_1.4.2 purrr_0.3.4
#> [63] BiocVersion_3.14.0 fastmap_1.1.0
#> [65] yaml_2.2.1 AnnotationDbi_1.55.1
#> [67] BiocManager_1.30.16 memoise_2.0.0
#> [69] knitr_1.34 sass_0.4.0