The TransOmicsData package contains datasets spanning various biological contexts such as in vitro embryonic and tissue-specific development in mouse and human. It covers multiple omics sequencing technologies such as RNAseq, mass spectrometry and ChIP-seq. This package was developed to provide convenient access to raw or pre-processed data for comparative trans-omics analysis.
The data stored in this package can be retrieved using ExperimentHub.
# if (!requireNamespace("BiocManager", quietly = TRUE))
# install.packages("BiocManager")
# BiocManager::install("ExperimentHub")library(ExperimentHub)
refreshHub(hubClass = "ExperimentHub")## ExperimentHub with 8333 records
## # snapshotDate(): 2024-10-24
## # $dataprovider: Eli and Edythe L. Broad Institute of Harvard and MIT, NCBI,...
## # $species: Homo sapiens, Mus musculus, Saccharomyces cerevisiae, Drosophila...
## # $rdataclass: SummarizedExperiment, data.frame, ExpressionSet, matrix, char...
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## # rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["EH1"]]'
##
## title
## EH1 | RNA-Sequencing and clinical data for 7706 tumor samples from The...
## EH166 | ERR188297
## EH167 | ERR188088
## EH168 | ERR188204
## EH169 | ERR188317
## ... ...
## EH9604 | Resistance of TEAD inhibitor to drug
## EH9605 | spe
## EH9606 | sce
## EH9607 | ProteinGym metadata for 217 DMS substitution assays
## EH9608 | roadmap_wgbs_hg38ehub <- ExperimentHub()
myfiles <- query(ehub, "TransOmicsData")
myfiles## ExperimentHub with 12 records
## # snapshotDate(): 2024-10-24
## # $dataprovider: PRIDE, NCBI
## # $species: Mus musculus, Homo sapiens
## # $rdataclass: SummarizedExperiment
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## # rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["EH8536"]]'
##
## title
## EH8536 | Chen organoid phosphoproteome
## EH8537 | Chen organoid proteome
## EH8538 | Chen organoid transcriptome
## EH8539 | Xiao myogenesis differentation phosphoproteome
## EH8540 | Xiao myogenesis differentiation proteome
## ... ...
## EH8543 | Yang ESC epigenome
## EH8544 | Yang ESC phosphoproteome
## EH8545 | Yang ESC proteome
## EH8546 | Yang ESC transcriptome
## EH9515 | Chen organoid sctranscriptome# BiocManager::install("TransOmicsData")To list the summarized metadata for all datasets in the package:
library(TransOmicsData)
listDatasets()## DataFrame with 3 rows and 5 columns
## Title Description Omics Species
## <character> <character> <character> <character>
## 1 chen-organoid neural organoid diff.. phosphoproteome, pro.. human
## 2 xiao-myogenesis C2C12 myogenesis dif.. phosphoproteome, pro.. mouse
## 3 yang-esc ESC to epiLC differe.. epigenome, phosphopr.. human
## RDataPath
## <character>
## 1 TransOmicsData/0.99...
## 2 TransOmicsData/0.99...
## 3 TransOmicsData/0.99...TransOmicsDataWe hope that TransOmicsData will be useful for your research. Please use the following information to cite the package. Thank you!
## Citation info
citation("TransOmicsData")## To cite TransOmicsData in publications use:
##
## Chen C, Xiao D, Yang P (2024). _TransOmicsData: a collection of
## trans-omics data covering a wide range of biological systems._.
## University of Sydney, Sydney, Australia.
## doi:10.18129/B9.bioc.TransOmicsData
## <https://doi.org/10.18129/B9.bioc.TransOmicsData>,
## <https://github.com/PYangLab/TransOmicsData>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {TransOmicsData: a collection of trans-omics data covering a wide range of biological systems.},
## author = {Carissa Chen and Di Xiao and Pengyi Yang},
## organization = {University of Sydney},
## address = {Sydney, Australia},
## year = {2024},
## url = {https://github.com/PYangLab/TransOmicsData},
## doi = {10.18129/B9.bioc.TransOmicsData},
## }## R Under development (unstable) (2024-10-21 r87258)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C 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] TransOmicsData_1.3.0 ExperimentHub_2.15.0 AnnotationHub_3.15.0 BiocFileCache_2.15.0 dbplyr_2.5.0
## [6] BiocGenerics_0.53.1 generics_0.1.3 BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] KEGGREST_1.47.0 xfun_0.49 bslib_0.8.0 Biobase_2.67.0
## [5] vctrs_0.6.5 tools_4.5.0 stats4_4.5.0 curl_5.2.3
## [9] tibble_3.2.1 fansi_1.0.6 AnnotationDbi_1.69.0 RSQLite_2.3.7
## [13] blob_1.2.4 pkgconfig_2.0.3 S4Vectors_0.45.0 lifecycle_1.0.4
## [17] GenomeInfoDbData_1.2.13 compiler_4.5.0 Biostrings_2.75.0 GenomeInfoDb_1.43.0
## [21] htmltools_0.5.8.1 sass_0.4.9 yaml_2.3.10 pillar_1.9.0
## [25] crayon_1.5.3 jquerylib_0.1.4 cachem_1.1.0 mime_0.12
## [29] tidyselect_1.2.1 digest_0.6.37 dplyr_1.1.4 purrr_1.0.2
## [33] bookdown_0.41 BiocVersion_3.21.1 fastmap_1.2.0 cli_3.6.3
## [37] magrittr_2.0.3 utf8_1.2.4 withr_3.0.2 filelock_1.0.3
## [41] UCSC.utils_1.3.0 rappdirs_0.3.3 bit64_4.5.2 rmarkdown_2.29
## [45] XVector_0.47.0 httr_1.4.7 bit_4.5.0 png_0.1-8
## [49] memoise_2.0.1 evaluate_1.0.1 knitr_1.48 IRanges_2.41.0
## [53] rlang_1.1.4 glue_1.8.0 DBI_1.2.3 BiocManager_1.30.25
## [57] jsonlite_1.8.9 R6_2.5.1 zlibbioc_1.53.0