DoubleExpSeq
Differential Exon Usage Test for RNA-Seq Data via Empirical Bayes Shrinkage of the Dispersion Parameter
Description
Differential exon usage test for RNA-Seq data via an empirical Bayes shrinkage method for the dispersion parameter the utilizes inclusion-exclusion data to analyze the propensity to skip an exon across groups. The input data consists of two matrices where each row represents an exon and the columns represent the biological samples. The first matrix is the count of the number of reads expressing the exon for each sample. The second matrix is the count of the number of reads that either express the exon or explicitly skip the exon across the samples, a.k.a. the total count matrix. Dividing the two matrices yields proportions representing the propensity to express the exon versus skipping the exon for each sample.
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CRAN Check Status
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | NOTE |
| r-devel-linux-x86_64-debian-gcc | NOTE |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (2 non-OK)
CRAN incoming feasibility
Maintainer: ‘Sean Ruddy <s.ruddy@yahoo.com>’
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CRAN incoming feasibility
Maintainer: ‘Sean Ruddy <s.ruddy@yahoo.com>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = "Sean",
family = "Ruddy",
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email = "s.ruddy@yahoo.com")
as necessary.
Check History
NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
CRAN incoming feasibility
Maintainer: ‘Sean Ruddy <s.ruddy@yahoo.com>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = "Sean",
family = "Ruddy",
role = c("aut", "cre"),
email = "s.ruddy@yahoo.com")
as necessary.
CRAN incoming feasibility
Maintainer: ‘Sean Ruddy <s.ruddy@yahoo.com>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = "Sean",
family = "Ruddy",
role = c("aut", "cre"),
email = "s.ruddy@yahoo.com")
as necessary.
Code
Structure
Lines of code
947
Files
20
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
1
Internal functions
3
Recent export changes
Testing & CI
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Return-value doc rate
–
\dontrun example ratio
0%
Roxygen coverage
–
Has pkgdown
No
NEWS present
No
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
2
First release
2014-05-13
Latest release
2015-09-04
Avg cadence
479 days
Cold removal rate
–
Dep drift
5
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/cran-code-metrics.