DOTSeq
1.0.0BioconductorGenome-wide Detection of Differential ORF Usage
- Bioconductor build, method
Method
Checks and health
CRAN runs every current package through
R CMD checkon a set of machines and publishes a result for each one. The health shown on a package page comes from these results alone.- Problems
- Notes alone never count against a package, but a warning, an error or a failure on any platform is a problem. Open CRAN deadlines are a fact of their own, shown as a clock after the mark, so the mark always says what the checks found.
- Checks only
- Health reflects CRAN's check results and nothing else. Even a package with no tests, no coverage or no recent release can have every platform OK.
- Once a day
- Results are collected once a day from files CRAN publishes. Each platform is one machine set-up, named by its R version, operating system, architecture and compiler, such as r-devel-linux-x86_64-fedora-clang.
- Platforms counted
- The 13 in 3 of 13 is the number of platform rows CRAN published for that package on the day of collection. The set of machines changes over time, so the number is not fixed, and a package missing from a platform counts as neither passing nor failing there.
- OKrelease 3.23
- Distinct IPs a month, method
- 371Rank 2,342 in its category
- Dependent packages, method
Method
Reverse dependencies
Dependent packages are other packages that list this one under
Depends,ImportsorLinkingToin theirDESCRIPTIONfile. Those fields list the packages a package needs to install, so dependents break if this one is archived or broken.- As declared
- The counts follow the declarations as written, not whether a package uses the other one when it runs.
- Suggests apart
- Packages that list this one only under
Suggestsinstall and run without it, and use it for tests, examples or an optional feature. They are counted as Suggested by, never among the dependents, and a package that also lists it under one of the three fields is a dependent and is not counted again. - Zero
- Zero dependents means no current CRAN package declares a need for this one, though some may suggest it. On 31 Oct 2026, 19,604 of the 25,610 current CRAN packages had no dependent package.
- 0none suggest it
- Bioconductor releases
- 1since 2026
- Advisories, method
Method
Security advisories
Advisories come from the R Consortium advisory database, a community record of security problems in R packages, as OSV publishes it.
- The copy
- The record is read once a day. The data is published under the Apache License 2.0 and is credited on the advisories list.
- Box under the name
- Under the package's name, a box names any advisory that affects the current release, with its fix or that there is none.
- Ranges
- Advisories state ranges, such as from 0.9.12 up to but not including 1.8.8. Each range is checked against every version CRAN has published, using the version rules R itself uses, so a release that came out after the advisory was written is still caught by its range.
- Not the package
- The rating is for the library flaw itself, not for how exposed the R package is, and it is never added up into a figure for the package.
- None publishedfor Bioconductor
About
Method, About Method Licence figures come from the Licences
License field of each package's DESCRIPTION file, read the way R itself reads it. No licence file is opened.tools::analyze_license() and R's own licence database, as CRAN's checks read it.| is read, so one string can offer two families.
Differential open reading frame (ORF) translation analysis framework for ribosome profiling (Ribo-seq) with matched RNA-seq.
Full description
Differential open reading frame (ORF) translation analysis framework for ribosome profiling (Ribo-seq) with matched RNA-seq. Implements (i) Differential ORF Usage (DOU), a beta-binomial generalized linear model that models the expected proportion of Ribo-seq versus RNA-seq reads mapping to each ORF within a gene, and (ii) ORF-level Differential Translation Efficiency (DTE), a negative binomial GLM that capture changes in translation efficiency of individual ORFs across experimental conditions. Supports ORF-level read summarization for bulk and single-cell Ribo-seq.
- Maintainer
- Chun Shen Lim
- Licence
- MIT + file LICENSE
- Last updated
- 28 Apr 2026
- First release
- Bioconductor 3.23, 29 Apr 2026
More details
- Releases
- 1 of 49 Bioconductor releases
- Category
- software
- RoxygenNote
- 7.3.3
biocViews (12)
Cite
Package
Run in R for the authors' entry:
citation("DOTSeq")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1101/2025.09.24.678201.
R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
Balamuta, J. J. (2026). R Observatory: Metrics for DOTSeq version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-10-31. https://doi.org/10.5281/zenodo.21843040
About
From data release v2026-10-31, which the citation names so these numbers can be found later.
Health
Release 3.23: OK 29 Oct 2026
kunpeng2, InstallInstall on the build machine kunpeng2. Bioconductor release 3.23.
OK
- Version built
- 1.0.0
- In this state since
- 29 Sep 2026 or earlier
- Last seen
- 29 Oct 2026
kunpeng2, BuildBuild on the build machine kunpeng2. Bioconductor release 3.23.
OK
- Version built
- 1.0.0
- In this state since
- 29 Sep 2026 or earlier
- Last seen
- 29 Oct 2026
kunpeng2, CheckCheck on the build machine kunpeng2. Bioconductor release 3.23.
OK
- Version built
- 1.0.0
- In this state since
- 29 Sep 2026 or earlier
- Last seen
- 29 Oct 2026
nebbiolo1, InstallInstall on the build machine nebbiolo1. Bioconductor release 3.23.
OK
- Version built
- 1.0.0
- In this state since
- 29 Sep 2026 or earlier
- Last seen
- 29 Oct 2026
nebbiolo1, BuildBuild on the build machine nebbiolo1. Bioconductor release 3.23.
OK
- Version built
- 1.0.0
- In this state since
- 29 Sep 2026 or earlier
- Last seen
- 29 Oct 2026
nebbiolo1, CheckCheck on the build machine nebbiolo1. Bioconductor release 3.23.
OK
- Version built
- 1.0.0
- In this state since
- 29 Sep 2026 or earlier
- Last seen
- 29 Oct 2026
- 6 OK
Machines (2)
| Machine | Install | Build | Check |
|---|---|---|---|
| kunpeng2 | OK | OK | OK |
| nebbiolo1 | OK | OK | OK |
Devel 3.24: OK
lconway, InstallInstall on the build machine lconway. The next Bioconductor release, 3.24.
OK
- Version built
- 1.1.0
- In this state since
- 29 Sep 2026 or earlier
- Last seen
- 28 Oct 2026
lconway, BuildBuild on the build machine lconway. The next Bioconductor release, 3.24.
OK
- Version built
- 1.1.0
- In this state since
- 29 Sep 2026 or earlier
- Last seen
- 28 Oct 2026
lconway, CheckCheck on the build machine lconway. The next Bioconductor release, 3.24.
OK
- Version built
- 1.1.0
- In this state since
- 29 Sep 2026 or earlier
- Last seen
- 28 Oct 2026
lconway, Build binaryBuild binary on the build machine lconway. The next Bioconductor release, 3.24.
OK
- Version built
- 1.1.0
- In this state since
- 29 Sep 2026 or earlier
- Last seen
- 28 Oct 2026
nebbiolo2, InstallInstall on the build machine nebbiolo2. The next Bioconductor release, 3.24.
OK
- Version built
- 1.1.0
- In this state since
- 29 Sep 2026 or earlier
- Last seen
- 29 Oct 2026
nebbiolo2, BuildBuild on the build machine nebbiolo2. The next Bioconductor release, 3.24.
OK
- Version built
- 1.1.0
- In this state since
- 29 Sep 2026 or earlier
- Last seen
- 29 Oct 2026
nebbiolo2, CheckCheck on the build machine nebbiolo2. The next Bioconductor release, 3.24.
OK
- Version built
- 1.1.0
- In this state since
- 29 Sep 2026 or earlier
- Last seen
- 29 Oct 2026
taishan, InstallInstall on the build machine taishan. The next Bioconductor release, 3.24.
OK
- Version built
- 1.1.0
- In this state since
- 29 Sep 2026 or earlier
- Last seen
- 29 Oct 2026
taishan, BuildBuild on the build machine taishan. The next Bioconductor release, 3.24.
OK
- Version built
- 1.1.0
- In this state since
- 29 Sep 2026 or earlier
- Last seen
- 29 Oct 2026
taishan, CheckCheck on the build machine taishan. The next Bioconductor release, 3.24.
OK
- Version built
- 1.1.0
- In this state since
- 29 Sep 2026 or earlier
- Last seen
- 29 Oct 2026
- 10 OK
| Machine | Install | Build | Check | Build binary |
|---|---|---|---|---|
| lconway | OK | OK | OK | OK |
| nebbiolo2 | OK | OK | OK | |
| taishan | OK | OK | OK |
Built files (4)
| Platform | Kind | File |
|---|---|---|
| macOS (Intel) | binary | DOTSeq_1.0.0.tgz |
| macOS (Apple Silicon) | binary | DOTSeq_1.0.0.tgz |
| source | source | DOTSeq_1.0.0.tar.gz |
| Windows | binary | DOTSeq_1.0.0.zip |
Downloads
Method, Downloads Method Download figures count requests logged by each distribution channel. They are not counts of installs or of users, because each channel publishes its own totals and this site reads them.Downloads
- Total downloads in the latest complete month
- 2,404It comes from Bioconductor alone. Bioconda was counted over another window, so it is not added.
Rank in category, by distinct IPs
2,342 of 3,173
Bioconductor
2,404 downloads in the latest complete month
Distinct IP addresses average 371 a month over 12 months, which is a different measure and is never added.
It is in the total. Take it out
Bioconda
11 downloads in the last 30 days
It is not added because it has no figure for the latest complete month.
The total is 2,404 downloads in the latest complete month. It comes from Bioconductor alone.
This local copy has no series over time.
Dependencies
- Needs
- 30
- Dependent packages
- 00 on CRAN, 0 on Bioconductor
- Suggested by
- 0
Needs (30)
- AnnotationDbi
- ashr
- BiocGenerics
- BiocParallel
- Biostrings
- boot
- BSgenome
- data.table
- DESeq2
- emmeans
- GenomeInfoDb
- GenomeInfoDbData
- GenomicAlignments
- GenomicFeatures
- GenomicRanges
- glmmTMB
- graphics
- grDevices
- IRanges
- Matrix
- methods
- pbapply
- Rcpp
- Rsamtools
- rtracklayer
- S4Vectors
- stats
- SummarizedExperiment
- txdbmaker
- utils
- Needed in total
- 157 packages
Code
Method, Code Method Code metrics come from reading the released source of each package version. The package is never installed, loaded or run.Code metrics
README, vignettes, a NEWS file and the shares read from its help pages. Files kept only in the repository, such as a pkgdown configuration or CI files, are read by the repository scan instead.
- Functions
- 81
- Public exports
- 24
- Lines of R code
- 9,719
- Median complexity
- 4
Functions (81)
Size and composition
Lines by kind (17,726)
| Kind | Lines | Share |
|---|---|---|
| R code | 9,719 | 55% |
| Tests | 1,873 | 11% |
| Documentation | 4,611 | 26% |
| Guides | 1,069 | 6% |
| Compiled code | 454 | 3% |
Lines by language
| Language | Lines | Share |
|---|---|---|
| R | 11,592 | 65% |
| Rd | 4,611 | 26% |
| Vignettes | 657 | 4% |
| C++ | 442 | 3% |
| Other | 412 | 2% |
| C | 12 | 0.1% |
Languages are counted from file extensions.
- Files
- 123
- R functions
- 67
- Compiled functions
- 14
- Object systems
- S4: 4 classes, S4: 11 generics, S4: 13 methods
Complexity
- Median
- 4
- Mean
- 8.84
- Highest
- 78
- Median lines per function
- 41
About complexity
Cyclomatic complexity counts the independent paths through a function: 1 is a straight line, higher is harder to test. R functions only.
Call graph figures
- R functions
- 67
- Calls
- 77
- Unconnected
- 4
- Groups
- 1
Tests
Method, Tests Method Test coverage is measured by downloading each CRAN package's current source file, installing its dependencies, building it and running its tests under covr.Test coverage
Test coverage is measured for CRAN packages only. Nothing is known for Bioconductor packages, which is not the same as no coverage.
- Test cases
- 62
- Lines of tests
- 1,873
- Exports named in tests
- 79.2%
- Has tests
- Yes
- Test frameworks
- testthat
- Test lines per line of code
- 0.19
Documentation
- Exports documented
- 100%
- Arguments documented
- 89.9%
- Return value documented
- 94.4%
- Help pages with examples
- 49.3%
- Examples run in checks
- 58.3%
Guides (1)
Other documentation
- README
- Yes, 369 words
- Release notes file
- Yes
- Help pages
- 73
- Lines of documentation
- 4,611
Datasets
Method, Datasets Method The datasets inside packages are read from their R objects in datasets
data/ folders when the code is analysed. Each object is described by its class, its shape and its columns, and fingerprinted so the same data can be found in other packages.data() are listed, 76,202 on CRAN and 8,045 on Bioconductor, so the list is not every file in data/.
2 datasets, 0 can be loaded by name
| Dataset | Size | Columns |
|---|---|---|
| featureCounts. | 6,642 × 1 | Geneid. |
| metadata | 23 × 5 | SRR24230462, rna, X2, chx, Mitotic_ |
People
Method, People Method People on the site are the names packages give them in their Author and maintainer identity
DESCRIPTION files: authors from the author list, and the maintainer from the Maintainer field. Spellings of one name become one person only where the rules below allow it, and when in doubt the rules keep people apart.
Repository
Method, figures by host Method Repository signals are the figures read from the source repository a package links to: stars, forks, issues, commits, releases and the time issues take to close. They are read from GitHub, GitLab, Codeberg and Bitbucket.Repository signals
URL and BugReports fields of its DESCRIPTION file. Read-only mirrors, the cran and bioc accounts on GitHub and git.bioconductor.org, are left out.
History
Method, History Method Archived is built from CRAN's archive records, its list of check deadlines and Bioconductor's package records. Every figure is counted to 31 Oct 2026, the day the data was read.Packages leaving
- In Bioconductor
- Bioconductor release
| Release | Released | R |
|---|---|---|
| 3.23 current | 29 Apr 2026 | 4.6 |
- Entered Bioconductor
- Release 3.23, 29 Apr 2026