The DNA Zoo Consortium is a collaborative group whose aim is to correct and refine genome assemblies across the tree of life using Hi-C approaches. As of 2023, they have performed Hi-C across more than 300 animal, plant and fungi species.
DNAZooData is a package giving programmatic access
to these uniformly processed Hi-C contact files, as well as the refined genome
assemblies.
The DNAZooData() function provides a gateway to DNA Zoo-hosted Hi-C files,
fetching and caching relevant contact matrices in .hic format, and
providing a direct URL to corrcted genome assemblies in fasta format.
It returns a HicFile object, which can then be imported in memory using
HiCExperiment::import().
HiCFile metadata also points to a URL to directly fetch the genome assembly
corrected by the DNA Zoo consortium.
library(DNAZooData)
head(DNAZooData())
#> species readme
#> 1 Acinonyx_jubatus Acinonyx_jubatus/README.json
#> 2 Acropora_millepora Acropora_millepora/README.json
#> 3 Addax_nasomaculatus Addax_nasomaculatus/README.json
#> 4 Aedes_aegypti Aedes_aegypti/README.json
#> 5 Aedes_aegypti__AaegL4 Aedes_aegypti__AaegL4/README.json
#> 6 Aedes_aegypti__AaegL5.0 Aedes_aegypti__AaegL5.0/README.json
#> readme_link
#> 1 https://dnazoo.s3.wasabisys.com/Acinonyx_jubatus/README.json
#> 2 https://dnazoo.s3.wasabisys.com/Acropora_millepora/README.json
#> 3 https://dnazoo.s3.wasabisys.com/Addax_nasomaculatus/README.json
#> 4 https://dnazoo.s3.wasabisys.com/Aedes_aegypti/README.json
#> 5 https://dnazoo.s3.wasabisys.com/Aedes_aegypti__AaegL4/README.json
#> 6 https://dnazoo.s3.wasabisys.com/Aedes_aegypti__AaegL5.0/README.json
#> original_assembly new_assembly
#> 1 aciJub1 aciJub1_HiC
#> 2 amil_sf_1.1 amil_sf_1.1_HiC
#> 3 ASM1959352v1 ASM1959352v1_HiC
#> 4 AGWG.draft AaegL5.0
#> 5 AaegL3 AaegL4
#> 6 AGWG.draft AaegL5.0
#> new_assembly_link
#> 1 https://dnazoo.s3.wasabisys.com/Acinonyx_jubatus/aciJub1_HiC.fasta.gz
#> 2 https://dnazoo.s3.wasabisys.com/Acropora_millepora/amil_sf_1.1_HiC.fasta.gz
#> 3 https://dnazoo.s3.wasabisys.com/Addax_nasomaculatus/ASM1959352v1_HiC.fasta.gz
#> 4 https://dnazoo.s3.wasabisys.com/Aedes_aegypti/AaegL5.0.fasta.gz
#> 5 https://dnazoo.s3.wasabisys.com/Aedes_aegypti__AaegL4/AaegL4.fasta.gz
#> 6 https://dnazoo.s3.wasabisys.com/Aedes_aegypti__AaegL5.0/AaegL5.0.fasta.gz
#> new_assembly_link_status
#> 1 200
#> 2 200
#> 3 200
#> 4 404
#> 5 200
#> 6 200
#> hic_link
#> 1 https://dnazoo.s3.wasabisys.com/Acinonyx_jubatus/aciJub1.rawchrom.hic
#> 2 https://dnazoo.s3.wasabisys.com/Acropora_millepora/amil_sf_1.1_HiC.hic
#> 3 https://dnazoo.s3.wasabisys.com/Addax_nasomaculatus/ASM1959352v1_HiC.hic
#> 4 <NA>
#> 5 https://dnazoo.s3.wasabisys.com/Aedes_aegypti__AaegL4/AaegL4.hic
#> 6 https://dnazoo.s3.wasabisys.com/Aedes_aegypti__AaegL5.0/AaegL5.0.hic
hicfile <- DNAZooData(species = 'Hypsibius_dujardini')
S4Vectors::metadata(hicfile)$organism
#> $vernacular
#> [1] "Tardigrade"
#>
#> $binomial
#> [1] "Hypsibius dujardini"
#>
#> $funFact
#> [1] "<i>Hypsibius dujardini</i> is a species of tardigrade, a tiny microscopic organism. They are also commonly called water bears. This species is found world-wide!"
#>
#> $extraInfo
#> [1] "on BioKIDS website"
#>
#> $extraInfoLink
#> [1] "http://www.biokids.umich.edu/critters/Hypsibius_dujardini/"
#>
#> $image
#> [1] "https://static.wixstatic.com/media/2b9330_82db39c219f24b20a75cb38943aad1fb~mv2.jpg"
#>
#> $imageCredit
#> [1] "By Willow Gabriel, Goldstein Lab - https://www.flickr.com/photos/waterbears/1614095719/ Template:Uploader Transferred from en.wikipedia to Commons., CC BY-SA 2.5, https://commons.wikimedia.org/w/index.php?curid=2261992"
#>
#> $isChromognomes
#> [1] "FALSE"
#>
#> $taxonomy
#> [1] "Species:202423-914154-914155-914158-155166-155362-710171-710179-710192-155390-155420"
S4Vectors::metadata(hicfile)$assemblyURL
#> [1] "https://dnazoo.s3.wasabisys.com/Hypsibius_dujardini/nHd_3.1_HiC.fasta.gz"DNAZooData package can be installed from Bioconductor using the following
command:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DNAZooData")The HiCExperiment package can be used to import .hic files provided by
DNAZooData. Refer to HiCExperiment package documentation for further
information.
availableResolutions(hicfile)
#> resolutions(9): 5000 10000 ... 1e+06 2500000
#>
availableChromosomes(hicfile)
#> Seqinfo object with 5 sequences from an unspecified genome:
#> seqnames seqlengths isCircular genome
#> HiC_scaffold_1 24848249 NA <NA>
#> HiC_scaffold_2 19596306 NA <NA>
#> HiC_scaffold_3 18943121 NA <NA>
#> HiC_scaffold_4 17897025 NA <NA>
#> HiC_scaffold_5 16309062 NA <NA>
x <- import(hicfile, resolution = 10000, focus = 'HiC_scaffold_4')
x
#> `HiCExperiment` object with 435,341 contacts over 1,790 regions
#> -------
#> fileName: "/home/biocbuild/.cache/R/DNAZooData/19e6c13ef79353_nHd_3.1_HiC.hic"
#> focus: "HiC_scaffold_4"
#> resolutions(9): 5000 10000 ... 1e+06 2500000
#> active resolution: 10000
#> interactions: 167314
#> scores(2): count balanced
#> topologicalFeatures: compartments(0) borders(0) loops(0) viewpoints(0)
#> pairsFile: N/A
#> metadata(6): organism draftAssembly ... credits assemblyURL
interactions(x)
#> GInteractions object with 167314 interactions and 4 metadata columns:
#> seqnames1 ranges1 seqnames2
#> <Rle> <IRanges> <Rle>
#> [1] HiC_scaffold_4 1-10000 --- HiC_scaffold_4
#> [2] HiC_scaffold_4 1-10000 --- HiC_scaffold_4
#> [3] HiC_scaffold_4 1-10000 --- HiC_scaffold_4
#> [4] HiC_scaffold_4 1-10000 --- HiC_scaffold_4
#> [5] HiC_scaffold_4 1-10000 --- HiC_scaffold_4
#> ... ... ... ... ...
#> [167310] HiC_scaffold_4 17870001-17880000 --- HiC_scaffold_4
#> [167311] HiC_scaffold_4 17870001-17880000 --- HiC_scaffold_4
#> [167312] HiC_scaffold_4 17880001-17890000 --- HiC_scaffold_4
#> [167313] HiC_scaffold_4 17880001-17890000 --- HiC_scaffold_4
#> [167314] HiC_scaffold_4 17890001-17897025 --- HiC_scaffold_4
#> ranges2 | bin_id1 bin_id2 count balanced
#> <IRanges> | <numeric> <numeric> <numeric> <numeric>
#> [1] 1-10000 | 6340 6340 20 162.01923
#> [2] 10001-20000 | 6340 6341 4 10.97758
#> [3] 20001-30000 | 6340 6342 1 2.82559
#> [4] 30001-40000 | 6340 6343 1 3.00288
#> [5] 80001-90000 | 6340 6348 1 2.63953
#> ... ... . ... ... ... ...
#> [167310] 17880001-17890000 | 8127 8128 4 3.91164
#> [167311] 17890001-17897025 | 8127 8129 4 7.35998
#> [167312] 17880001-17890000 | 8128 8128 107 99.46175
#> [167313] 17890001-17897025 | 8128 8129 8 13.99203
#> [167314] 17890001-17897025 | 8129 8129 47 154.67041
#> -------
#> regions: 1790 ranges and 3 metadata columns
#> seqinfo: 5 sequences from an unspecified genome
as(x, 'ContactMatrix')
#> class: ContactMatrix
#> dim: 1790 1790
#> type: dgCMatrix
#> rownames: NULL
#> colnames: NULL
#> metadata(0):
#> regions: 1790sessionInfo()
#> R version 4.4.0 beta (2024-04-15 r86425)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 22.04.4 LTS
#>
#> Matrix products: default
#> BLAS: /home/biocbuild/bbs-3.19-bioc/R/lib/libRblas.so
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_GB 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
#>
#> time zone: America/New_York
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] DNAZooData_1.4.0 HiCExperiment_1.4.0 BiocStyle_2.32.0
#>
#> loaded via a namespace (and not attached):
#> [1] SummarizedExperiment_1.34.0 rjson_0.2.21
#> [3] xfun_0.43 bslib_0.7.0
#> [5] rhdf5_2.48.0 Biobase_2.64.0
#> [7] lattice_0.22-6 tzdb_0.4.0
#> [9] rhdf5filters_1.16.0 vctrs_0.6.5
#> [11] tools_4.4.0 generics_0.1.3
#> [13] curl_5.2.1 stats4_4.4.0
#> [15] parallel_4.4.0 RSQLite_2.3.6
#> [17] tibble_3.2.1 fansi_1.0.6
#> [19] blob_1.2.4 pkgconfig_2.0.3
#> [21] Matrix_1.7-0 dbplyr_2.5.0
#> [23] S4Vectors_0.42.0 lifecycle_1.0.4
#> [25] GenomeInfoDbData_1.2.12 compiler_4.4.0
#> [27] codetools_0.2-20 InteractionSet_1.32.0
#> [29] GenomeInfoDb_1.40.0 htmltools_0.5.8.1
#> [31] sass_0.4.9 yaml_2.3.8
#> [33] pillar_1.9.0 crayon_1.5.2
#> [35] jquerylib_0.1.4 BiocParallel_1.38.0
#> [37] DelayedArray_0.30.0 cachem_1.0.8
#> [39] abind_1.4-5 tidyselect_1.2.1
#> [41] digest_0.6.35 purrr_1.0.2
#> [43] dplyr_1.1.4 bookdown_0.39
#> [45] fastmap_1.1.1 grid_4.4.0
#> [47] cli_3.6.2 SparseArray_1.4.0
#> [49] magrittr_2.0.3 S4Arrays_1.4.0
#> [51] utf8_1.2.4 withr_3.0.0
#> [53] filelock_1.0.3 UCSC.utils_1.0.0
#> [55] bit64_4.0.5 rmarkdown_2.26
#> [57] XVector_0.44.0 httr_1.4.7
#> [59] matrixStats_1.3.0 bit_4.0.5
#> [61] memoise_2.0.1 evaluate_0.23
#> [63] knitr_1.46 GenomicRanges_1.56.0
#> [65] IRanges_2.38.0 BiocIO_1.14.0
#> [67] BiocFileCache_2.12.0 rlang_1.1.3
#> [69] Rcpp_1.0.12 DBI_1.2.2
#> [71] glue_1.7.0 BiocManager_1.30.22
#> [73] BiocGenerics_0.50.0 vroom_1.6.5
#> [75] jsonlite_1.8.8 strawr_0.0.91
#> [77] R6_2.5.1 Rhdf5lib_1.26.0
#> [79] MatrixGenerics_1.16.0 zlibbioc_1.50.0