Background | Getting started | Searching for datasets of interest starting with accession numbers | Fetching DEE2 data using SRA run accession numbers | Downstream analysis | Legacy function | Large project bundles | Session Info
Package: getDEE2 1.23.0
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_1.23.0.tar.gz
getDEE2_1.23.0.zip(r-4.7)getDEE2_1.23.0.zip(r-4.6)getDEE2_1.23.0.zip(r-4.5)
getDEE2_1.23.0.tgz(r-4.6-any)getDEE2_1.23.0.tgz(r-4.5-any)
getDEE2_1.23.0.tar.gz(r-4.7-any)getDEE2_1.23.0.tar.gz(r-4.6-any)
getDEE2_1.23.0.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.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:aa86defccc. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 173 | ||
| linux-devel-x86_64 | NOTE | 397 | ||
| source / vignettes | OK | 275 | ||
| linux-release-x86_64 | NOTE | 425 | ||
| macos-release-arm64 | NOTE | 254 | ||
| macos-oldrel-arm64 | NOTE | 219 | ||
| windows-devel | NOTE | 245 | ||
| windows-release | NOTE | 255 | ||
| windows-oldrel | NOTE | 253 | ||
| wasm-release | OK | 116 |
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 |
