Package: getDEE2 1.17.0
Mark Ziemann
getDEE2: Programmatic access to the DEE2 RNA expression dataset
Digital Expression Explorer 2 (or DEE2 for short) is a repository of processed RNA-seq data in the form of counts. It was designed so that researchers could undertake re-analysis and meta-analysis of published RNA-seq studies quickly and easily. As of April 2020, over 1 million SRA datasets have been processed. This package provides an R interface to access these expression data. More information about the DEE2 project can be found at the project homepage (http://dee2.io) and main publication (https://doi.org/10.1093/gigascience/giz022).
Authors:
getDEE2_1.17.0.tar.gz
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getDEE2.pdf |getDEE2.html✨
getDEE2/json (API)
NEWS
| # Install 'getDEE2' in R: |
| install.packages('getDEE2', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/markziemann/getdee2/issues
On BioConductor:getDEE2-1.15.0(bioc 3.20)getDEE2-1.14.0(bioc 3.19)
geneexpressiontranscriptomicssequencingbioinformaticsdata-mininggenomicsrna-expressionrna-seq
Last updated 23 days agofrom:a598524d22. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 31 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | NOTE | Oct 31 2024 |
| R-4.3-mac | NOTE | Oct 31 2024 |
Exports:getDEE2getDEE2_bundlegetDEE2Metadatalist_bundlesloadFullMetaloadGeneCountsloadGeneInfoloadQcMxloadSummaryMetaloadTxCountsloadTxInfoquery_bundlesqueryDEE2sesrx_aggTx2Gene
Dependencies:abindaskpassBiobaseBiocGenericscrayoncurlDelayedArrayGenomeInfoDbGenomeInfoDbDataGenomicRangeshtm2txthttrIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6S4ArraysS4VectorsSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| getDEE2: Programmatic access to the DEE2 RNA expression dataset | getDEE2 |
| Get a DEE2 project bundle | getDEE2_bundle |
| Get DEE2 Metadata | getDEE2Metadata |
| Get a table of all completed projects at DEE2 | list_bundles |
| Load Full Metadata | loadFullMeta |
| Load Gene Counts | loadGeneCounts |
| Load Gene Info | loadGeneInfo |
| Load Quality Control Info | loadQcMx |
| Load Summary Metadata | loadSummaryMeta |
| Load Transcript Counts | loadTxCounts |
| Load Transcript Info | loadTxInfo |
| Query whether a project bundle is available from DEE2 | query_bundles |
| Query Whether a DEE2 Dataset is Available | queryDEE2 |
| Create summarizedExperiment object | se |
| Summarized run data to experiments | srx_agg |
| Aggregate Transcript Counts to Gene-Level Counts | Tx2Gene |
