recount
Bioc currentExplore and download data from the recount project
Release Lineage
Entered 3.4 · Oct 18, 2016
Current · Requires R 4.6
Description
Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
20 18 exported
Complexity
5.3 avg / 12 max
Call network
20 nodes / 11 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
4,787
Files
69
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
18
Internal functions
2
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.16
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
6.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.3.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
20
First release
2017-03-21
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 24 (1 internal)includes a package overview page
- Examples that run
- 94%17 run in a plain check · 1 never run
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 42%
Repository practices
12 development-tooling and community-health practices detected across 5 families in the upstream repository
Checks run against github.com/leekgroup/recount on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-03-31 · The repository has a site deploy workflow
Show all practicesHide 1 practice
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| recount_abstract | data.frame | 2,041 × 4 | No other package |
| recount_exons | – | – | – |
| recount_genes | – | – | – |
| recount_url | data.frame | 97,229 × 6 | No other package |
| rse_gene_SRP009615 | – | – | – |
Topics
Depended on by (4)
Bioconductor (4)
People
- Leonardo Collado-Torres author maintainer
- Shannon E. Ellis contributor
- Kasper Daniel Hansen contributor
- Andrew E. Jaffe contributor
- Kai Kammers contributor
- Ben Langmead contributor
- Jeffrey T. Leek author thesis advisor
- Abhinav Nellore contributor
- Margaret A. Taub contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("recount")The package provides a citation file that builds its entry when R runs it. Run citation() to see it.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.