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Merged
igunduz merged 1 commit into from
Sep 29, 2026
Merged

Address Bioconductor review; bump version #35

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4 changes: 2 additions & 2 deletions CITATION.cff
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Original file line number Diff line number Diff line change
Expand Up @@ -18,8 +18,8 @@ authors:
- family-names: Mueller
given-names: Fabian
orcid: "https://orcid.org/0000-0001-5809-2321"
version: 0.99.8
date-released: "2026-08-19"
version: 0.99.9
date-released: "2026-09-29"
doi: 10.18129/B9.bioc.methylTFR
license: MIT
repository-code: "https://github.com/EpigenomeInformatics/methylTFR"
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4 changes: 2 additions & 2 deletions DESCRIPTION
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@@ -1,7 +1,7 @@
Package: methylTFR
Title: Quantification of DNA Methylation Signatures in TFBS
Version: 0.99.8
Date: 2026-08-19
Version: 0.99.9
Date: 2026-09-29
Authors@R: c(
person("Irem B.", "Gündüz", , "irembgunduz@gmail.com", role = c("aut", "cre"),
comment = c(ORCID = "0000-0003-2641-0916")),
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23 changes: 23 additions & 0 deletions NEWS.md
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@@ -1,3 +1,26 @@
# methylTFR 0.99.9

CHANGES

* `Authors@R` lists the funders (ERA-NET Transcan-Neu III - EPILUNAR,
grant 01KT2409; Saarland University NanoBioMed Young Investigator Grant)
with the `fnd` role.
* `inst/CITATION` rewritten: the citation reads "Gunduz IB, Murugan SK,
Mueller F (year). methylTFR: ... R package version x.y.z.", takes the
version and year from DESCRIPTION, and carries the Bioconductor DOI.
* The README shows the citation and BibTeX entry.
* Added `CITATION.cff` (excluded from the build via `.Rbuildignore`).

BUG FIXES

* `rnb_sample_ids()` no longer calls `RnBeads::samples()`, which is not
exported by all RnBeads versions (R CMD check: "Missing or unexported
object"). Sample identifiers are read from the `identifiers.column` of
`RnBeads::pheno()`, with the previous fallbacks unchanged.
* The vignette, README and `inst/scripts/vignette_data.R` call
`getGenomeGC()` without an argument, which works with every version of
the annotation packages.

# methylTFR 0.99.8

BUG FIXES
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4 changes: 2 additions & 2 deletions README.Rmd
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Expand Up @@ -80,14 +80,14 @@ deviations <- run_methyltfr(sample_ann, # sample annotation file

If you use `methylTFR` in your work, please cite:

> Gunduz IB, Murugan SK, Mueller F (2026). methylTFR: Quantification of DNA methylation signatures in TFBS. R package version 0.99.8. https://github.com/EpigenomeInformatics/methylTFR
> Gunduz IB, Murugan SK, Mueller F (2026). methylTFR: Quantification of DNA methylation signatures in TFBS. R package version 0.99.9. https://github.com/EpigenomeInformatics/methylTFR

```bibtex
@Manual{methylTFR,
title = {methylTFR: Quantification of DNA methylation signatures in TFBS},
author = {Irem B. Gunduz and Sarath Kumar Murugan and Fabian Mueller},
year = {2026},
note = {R package version 0.99.8},
note = {R package version 0.99.9},
url = {https://github.com/EpigenomeInformatics/methylTFR},
doi = {10.18129/B9.bioc.methylTFR},
}
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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -75,14 +75,14 @@ deviations <- run_methyltfr(sample_ann, # sample annotation file

If you use `methylTFR` in your work, please cite:

> Gunduz IB, Murugan SK, Mueller F (2026). methylTFR: Quantification of DNA methylation signatures in TFBS. R package version 0.99.8. https://github.com/EpigenomeInformatics/methylTFR
> Gunduz IB, Murugan SK, Mueller F (2026). methylTFR: Quantification of DNA methylation signatures in TFBS. R package version 0.99.9. https://github.com/EpigenomeInformatics/methylTFR

```bibtex
@Manual{methylTFR,
title = {methylTFR: Quantification of DNA methylation signatures in TFBS},
author = {Irem B. Gunduz and Sarath Kumar Murugan and Fabian Mueller},
year = {2026},
note = {R package version 0.99.8},
note = {R package version 0.99.9},
url = {https://github.com/EpigenomeInformatics/methylTFR},
doi = {10.18129/B9.bioc.methylTFR},
}
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