Package: getDEE2 1.22.0
Mark 0000-0002-7688-6974 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_1.22.0.tar.gz
getDEE2_1.22.0.zip(r-4.7-any)getDEE2_1.22.0.zip(r-4.6-any)getDEE2_1.22.0.zip(r-4.5-any)
getDEE2_1.22.0.tgz(r-4.6-any)getDEE2_1.22.0.tgz(r-4.5-any)
getDEE2_1.22.0.tar.gz(r-4.7-any)getDEE2_1.22.0.tar.gz(r-4.6-any)
getDEE2_1.22.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
getDEE2/json (API)
| # Install 'getDEE2' in R: |
| install.packages('getDEE2', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/markziemann/getdee2/issues
On BioConductor:getDEE2-1.23.0(bioc 3.24)getDEE2-1.22.0(bioc 3.23)
geneexpressiontranscriptomicssequencingbioinformaticsdata-mininggenomicsrna-expressionrna-seq
Last updated from:73153e297e (on RELEASE_3_23). Checks:1 NOTE, 3 ERROR, 5 WARNING, 1 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 181 | ||
| linux-devel-x86_64 | ERROR | 548 | ||
| source / vignettes | ERROR | 345 | ||
| linux-release-x86_64 | ERROR | 524 | ||
| macos-release-arm64 | WARNING | 209 | ||
| macos-oldrel-arm64 | WARNING | 229 | ||
| windows-devel | WARNING | 242 | ||
| windows-release | WARNING | 249 | ||
| windows-oldrel | WARNING | 229 | ||
| wasm-release | OK | 111 |
Exports:getDEE2getDEE2_bundlegetDEE2Metadatalist_bundlesloadFullMetaloadGeneCountsloadGeneInfoloadQcMxloadSummaryMetaloadTxCountsloadTxInfoquery_bundlesqueryDEE2sesrx_aggTx2Gene
Dependencies:abindBiobaseBiocGenericsDelayedArraygenericsGenomicRangeshtm2txtIRangeslatticeMatrixMatrixGenericsmatrixStatsS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector
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 |
