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 14 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-macos-arm64 | 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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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.
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.