Introduction
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"Installation
DNAZooData package can be installed from Bioconductor
using the following command:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DNAZooData")HiCExperiment and 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: "/github/home/.cache/R/DNAZooData/645479c03f93_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: 1790Session info
sessionInfo()
#> R version 4.3.0 (2023-04-21)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 22.04.2 LTS
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
#> [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: UTC
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] DNAZooData_1.1.0 HiCExperiment_1.1.0 BiocStyle_2.29.0
#>
#> loaded via a namespace (and not attached):
#> [1] SummarizedExperiment_1.31.0 rjson_0.2.21
#> [3] xfun_0.39 bslib_0.4.2
#> [5] rhdf5_2.45.0 Biobase_2.61.0
#> [7] lattice_0.21-8 tzdb_0.3.0
#> [9] rhdf5filters_1.13.1 vctrs_0.6.2
#> [11] tools_4.3.0 bitops_1.0-7
#> [13] generics_0.1.3 curl_5.0.0
#> [15] stats4_4.3.0 parallel_4.3.0
#> [17] RSQLite_2.3.1 tibble_3.2.1
#> [19] fansi_1.0.4 blob_1.2.4
#> [21] pkgconfig_2.0.3 Matrix_1.5-4
#> [23] dbplyr_2.3.2 desc_1.4.2
#> [25] S4Vectors_0.39.0 lifecycle_1.0.3
#> [27] GenomeInfoDbData_1.2.10 compiler_4.3.0
#> [29] stringr_1.5.0 textshaping_0.3.6
#> [31] codetools_0.2-19 InteractionSet_1.29.0
#> [33] GenomeInfoDb_1.37.0 htmltools_0.5.5
#> [35] sass_0.4.5 RCurl_1.98-1.12
#> [37] yaml_2.3.7 crayon_1.5.2
#> [39] pkgdown_2.0.7 pillar_1.9.0
#> [41] jquerylib_0.1.4 BiocParallel_1.35.0
#> [43] DelayedArray_0.27.0 cachem_1.0.7
#> [45] tidyselect_1.2.0 digest_0.6.31
#> [47] stringi_1.7.12 dplyr_1.1.2
#> [49] purrr_1.0.1 bookdown_0.33
#> [51] rprojroot_2.0.3 fastmap_1.1.1
#> [53] grid_4.3.0 cli_3.6.1
#> [55] magrittr_2.0.3 utf8_1.2.3
#> [57] withr_2.5.0 filelock_1.0.2
#> [59] bit64_4.0.5 httr_1.4.5
#> [61] rmarkdown_2.21 XVector_0.41.0
#> [63] matrixStats_0.63.0 bit_4.0.5
#> [65] ragg_1.2.5 memoise_2.0.1
#> [67] evaluate_0.20 knitr_1.42
#> [69] GenomicRanges_1.53.0 IRanges_2.35.0
#> [71] BiocIO_1.11.0 BiocFileCache_2.9.0
#> [73] rlang_1.1.0 Rcpp_1.0.10
#> [75] DBI_1.1.3 glue_1.6.2
#> [77] BiocManager_1.30.20 BiocGenerics_0.47.0
#> [79] vroom_1.6.1 jsonlite_1.8.4
#> [81] strawr_0.0.91 R6_2.5.1
#> [83] Rhdf5lib_1.23.0 MatrixGenerics_1.13.0
#> [85] systemfonts_1.0.4 fs_1.6.2
#> [87] zlibbioc_1.47.0