From 22b85e97f96ec40c9110ce35c73c1402542404ff Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Cigunduz=E2=80=9D?= Date: Tue, 29 Sep 2026 16:47:24 +0200 Subject: [PATCH] Address Bioconductor review; bump version --- CITATION.cff | 4 ++-- DESCRIPTION | 4 ++-- NEWS.md | 23 +++++++++++++++++++++++ README.Rmd | 4 ++-- README.md | 4 ++-- 5 files changed, 31 insertions(+), 8 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 2e50e64..0e114e5 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -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" diff --git a/DESCRIPTION b/DESCRIPTION index f95b550..0c4e8a7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -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")), diff --git a/NEWS.md b/NEWS.md index ac24e64..2c3f93c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -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 diff --git a/README.Rmd b/README.Rmd index bfe86c2..0d8ea10 100644 --- a/README.Rmd +++ b/README.Rmd @@ -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}, } diff --git a/README.md b/README.md index 9d94f79..d5ec20c 100644 --- a/README.md +++ b/README.md @@ -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}, }