From fa4b81a5fcc2103dd2bc46333889b8c60c15ed22 Mon Sep 17 00:00:00 2001 From: Federico Marini Date: Tue, 10 Feb 2026 16:54:35 +0100 Subject: [PATCH 1/9] add citation info in the README file(s) --- README.Rmd | 29 +++++++++++++++++++++++++++++ README.md | 49 ++++++++++++++++++++++++++++++++----------------- 2 files changed, 61 insertions(+), 17 deletions(-) diff --git a/README.Rmd b/README.Rmd index 202f954..dc01f4f 100644 --- a/README.Rmd +++ b/README.Rmd @@ -65,6 +65,35 @@ If you encounter a bug, have usage questions, or want to share ideas and functionality to make this package better, feel free to file an [issue](https://github.com/ingmbioinfo/CIA_R/issues). +## Citation + +To cite CIA in your work, please use: + +> Ferrari I, Battistella M, Vincenti F, Gobbini A, Marini F, Notarbartolo S, +Costanza J, Biffo S, Grifantini R, Abrignani S, Galeota E (2025). “CIA: +unveiling cellular identities with cluster-independent annotation in +single-cell RNA sequencing data for comprehensive cell type characterization +and exploration.” _BMC Bioinformatics_, *27*(38). +doi:10.1186/s12859-025-06320-z . + +or the BibTeX entry: + +``` +@article{Ferrari2025, + title = {CIA: unveiling cellular identities with cluster-independent annotation in single-cell RNA sequencing data for comprehensive cell type characterization and exploration}, + volume = {27}, + ISSN = {1471-2105}, + url = {http://dx.doi.org/10.1186/s12859-025-06320-z}, + DOI = {10.1186/s12859-025-06320-z}, + number = {38}, + journal = {BMC Bioinformatics}, + publisher = {Springer Science and Business Media LLC}, + author = {Ferrari, Ivan and Battistella, Mattia and Vincenti, Francesca and Gobbini, Andrea and Marini, Federico and Notarbartolo, Samuele and Costanza, Jole and Biffo, Stefano and Grifantini, Renata and Abrignani, Sergio and Galeota, Eugenia}, + year = {2025}, + month = dec +} +``` + ## Code of Conduct Please note that the CIA project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). diff --git a/README.md b/README.md index 157efee..222c057 100644 --- a/README.md +++ b/README.md @@ -50,37 +50,52 @@ integration into existing workflows. - **Python docs**: `CIA Python documentation `\_ - **R Package and Tutorial**: - `CIA R GitHub Repository `\_ + `CIA R GitHub Repository `\_ ## Installation You can install the development version of `CIA` from GitHub with: ``` r -if (!requireNamespace("BiocManager", quietly = TRUE)) - install.packages("BiocManager") -BiocManager::install("ingmbioinfo/CIA_R", force = TRUE, dependencies = TRUE) +library("remotes") +remotes::install_github("ingmbioinfo/CIA_R", + dependencies = TRUE, build_vignettes = TRUE) ``` -## Installation with conda - -You can also install the development version of `CIA` exploiting CIA_R.yml (in inst folder): - -``` bash - -conda env create -n {name} -f CIA_R.yml -conda activate {name} -Rscript -e 'if (!requireNamespace("remotes", quietly=TRUE)) install.packages("remotes", repos="https://cloud.r-project.org"); remotes::install_github("ingmbioinfo/CIA_R", dependencies=TRUE, upgrade="never", build_vignettes=FALSE)' - -``` - - ## Development If you encounter a bug, have usage questions, or want to share ideas and functionality to make this package better, feel free to file an [issue](https://github.com/ingmbioinfo/CIA_R/issues). +## Citation + +To cite CIA in your work, please use: + +> Ferrari I, Battistella M, Vincenti F, Gobbini A, Marini F, +> Notarbartolo S, Costanza J, Biffo S, Grifantini R, Abrignani S, +> Galeota E (2025). “CIA: unveiling cellular identities with +> cluster-independent annotation in single-cell RNA sequencing data for +> comprehensive cell type characterization and exploration.” *BMC +> Bioinformatics*, *27*(38). +> . + +or the BibTeX entry: + + @article{Ferrari2025, + title = {CIA: unveiling cellular identities with cluster-independent annotation in single-cell RNA sequencing data for comprehensive cell type characterization and exploration}, + volume = {27}, + ISSN = {1471-2105}, + url = {http://dx.doi.org/10.1186/s12859-025-06320-z}, + DOI = {10.1186/s12859-025-06320-z}, + number = {38}, + journal = {BMC Bioinformatics}, + publisher = {Springer Science and Business Media LLC}, + author = {Ferrari, Ivan and Battistella, Mattia and Vincenti, Francesca and Gobbini, Andrea and Marini, Federico and Notarbartolo, Samuele and Costanza, Jole and Biffo, Stefano and Grifantini, Renata and Abrignani, Sergio and Galeota, Eugenia}, + year = {2025}, + month = dec + } + ## Code of Conduct Please note that the CIA project is released with a [Contributor Code of From 3abc89969b5510930e8c257c47845e7f5f00599b Mon Sep 17 00:00:00 2001 From: Federico Marini Date: Tue, 10 Feb 2026 16:54:51 +0100 Subject: [PATCH 2/9] while at it, using a more up-to-date gmt from wikipathways --- R/CIA_core.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/CIA_core.R b/R/CIA_core.R index 2719722..f3a0110 100644 --- a/R/CIA_core.R +++ b/R/CIA_core.R @@ -26,7 +26,7 @@ #' signatures #' #' gmt_url <- -#' "https://data.wikipathways.org/20251110/gmt/wikipathways-20251110-gmt-Homo_sapiens.gmt" +#' "https://data.wikipathways.org/20260110/gmt/wikipathways-20260110-gmt-Homo_sapiens.gmt" #' #' sig_wikipathways <- load_signatures(gmt_url) #' head(names(sig_wikipathways)) From 5647604874ecdb8aab47336a87e5ae30bc0e1838 Mon Sep 17 00:00:00 2001 From: Federico Marini Date: Tue, 10 Feb 2026 16:55:00 +0100 Subject: [PATCH 3/9] re-rendered manpage --- man/load_signatures.Rd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/man/load_signatures.Rd b/man/load_signatures.Rd index 4dc0269..b7845ba 100644 --- a/man/load_signatures.Rd +++ b/man/load_signatures.Rd @@ -31,7 +31,7 @@ signatures <- load_signatures(gmt_file) signatures gmt_url <- - "https://data.wikipathways.org/20251110/gmt/wikipathways-20251110-gmt-Homo_sapiens.gmt" + "https://data.wikipathways.org/20260110/gmt/wikipathways-20260110-gmt-Homo_sapiens.gmt" sig_wikipathways <- load_signatures(gmt_url) head(names(sig_wikipathways)) From 5efc3718b317b9f5db284d7ef992ad74a90d0c42 Mon Sep 17 00:00:00 2001 From: Federico Marini Date: Tue, 10 Feb 2026 16:55:16 +0100 Subject: [PATCH 4/9] added inst/CITATION file for formal citation within the package usage --- inst/CITATION | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 inst/CITATION diff --git a/inst/CITATION b/inst/CITATION new file mode 100644 index 0000000..cc7569c --- /dev/null +++ b/inst/CITATION @@ -0,0 +1,24 @@ +bibentry( + bibtype = "Article", + title = "CIA: unveiling cellular identities with cluster-independent annotation in single-cell RNA sequencing data for comprehensive cell type characterization and exploration", + author = c( + person("Ivan", "Ferrari"), + person("Mattia", "Battistella"), + person("Francesca", "Vincenti"), + person("Andrea", "Gobbini"), + person("Federico", "Marini"), + person("Samuele", "Notarbartolo"), + person("Jole", "Costanza"), + person("Stefano", "Biffo"), + person("Renata", "Grifantini"), + person("Sergio", "Abrignani"), + person("Eugenia", "Galeota") + ), + journal = "BMC Bioinformatics", + publisher = "Springer Science and Business Media LLC", + year = "2025", + volume = "27", + url = "http://dx.doi.org/10.1186/s12859-025-06320-z", + number = "38", + doi = "10.1186/s12859-025-06320-z" +) From 5b823ac646255107f7a0bdcae50f163263355f1f Mon Sep 17 00:00:00 2001 From: Federico Marini Date: Tue, 10 Feb 2026 16:55:35 +0100 Subject: [PATCH 5/9] version bump, 0.3.2 --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0456014..8878d4d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: CIA Title: Cluster Independent Annotation (CIA) to Accurately Classify Cells in scRNA-seq Datasets Using Gene Signatures -Version: 0.3.1 +Version: 0.3.2 Authors@R: c( person( From 712ec93cfb50894f739d327ca2dc2556bcb6666b Mon Sep 17 00:00:00 2001 From: Federico Marini Date: Tue, 10 Feb 2026 17:00:34 +0100 Subject: [PATCH 6/9] add infos also in the vignette of the package --- vignettes/CIA_user_manual.Rmd | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/vignettes/CIA_user_manual.Rmd b/vignettes/CIA_user_manual.Rmd index 40e356d..6b327bc 100644 --- a/vignettes/CIA_user_manual.Rmd +++ b/vignettes/CIA_user_manual.Rmd @@ -88,6 +88,8 @@ This tool offers several advantages: # Getting started {#gettingstarted} +## Installation and usage of CIA + To install this package, start R and enter: ```{r install, eval=FALSE} @@ -109,6 +111,24 @@ If you want to install the development version (from the GitHub repository), you BiocManager::install("ingmbioinfo/CIA_R") ``` +## Citing CIA + +To cite CIA in your work, please use: + +> Ferrari I, Battistella M, Vincenti F, Gobbini A, Marini F, Notarbartolo S, +Costanza J, Biffo S, Grifantini R, Abrignani S, Galeota E (2025). “CIA: +unveiling cellular identities with cluster-independent annotation in +single-cell RNA sequencing data for comprehensive cell type characterization +and exploration.” _BMC Bioinformatics_, *27*(38). +doi:10.1186/s12859-025-06320-z . + +The full information, including a BibTeX entry, can be obtained as usual via + +```{r citation} +citation("CIA") +``` + + # CIA input {#inputtocia} Our method requires as input a **named list of gene signatures** (e.g. cell type, cell state ...) and a scRNA-seq data in **[SeuratObject](https://rdrr.io/cran/SeuratObject/) or [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) format**. From 520400a66918f834bea27105483517c9f96798c4 Mon Sep 17 00:00:00 2001 From: Federico Marini Date: Tue, 10 Feb 2026 17:14:05 +0100 Subject: [PATCH 7/9] updating GHA to use newest bioc version --- .github/workflows/R-CMD-check.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 4a37e3b..26bc378 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -52,9 +52,9 @@ jobs: fail-fast: false matrix: config: - - { os: ubuntu-latest, r: 'devel', bioc: '3.21', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" } - - { os: macOS-latest, r: 'devel', bioc: '3.21'} - - { os: windows-latest, r: 'devel', bioc: '3.21'} + - { os: ubuntu-latest, r: 'devel', bioc: '3.23', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" } + - { os: macOS-latest, r: 'devel', bioc: '3.23'} + - { os: windows-latest, r: 'devel', bioc: '3.23'} ## Check https://github.com/r-lib/actions/tree/master/examples ## for examples using the http-user-agent env: From e5d7a70dee65ba4106019a30fac28493b7966e1d Mon Sep 17 00:00:00 2001 From: Federico Marini Date: Tue, 10 Feb 2026 17:14:19 +0100 Subject: [PATCH 8/9] removing relevant freetype bit from GHA --- .github/workflows/R-CMD-check.yaml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 26bc378..bb0b79f 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -146,11 +146,6 @@ jobs: ## Required for terra brew install gdal - ## Temporary fix for freetype (https://github.com/r-lib/ragg/issues/170; Sep 2024) - #brew install --cask https://raw.githubusercontent.com/Homebrew/homebrew-core/d28afc3bfdb5d24eab02157bfffcc9e17ed6666c/Formula/f/freetype.rb - brew unlink freetype - curl -L https://raw.githubusercontent.com/Homebrew/homebrew-core/3db6dc6c4baf5a75e345f380cc4e8224c1ae5ae0/Formula/f/freetype.rb > freetype.rb && brew install freetype.rb - - name: Install binary units for macOS if: matrix.config.os == 'macOS-latest' run: | From 11ca673c3376be22f8044803a7bfffe025695592 Mon Sep 17 00:00:00 2001 From: Federico Marini Date: Tue, 10 Feb 2026 21:25:32 +0100 Subject: [PATCH 9/9] libintl error --- .github/workflows/R-CMD-check.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index bb0b79f..7bad5af 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -146,6 +146,9 @@ jobs: ## Required for terra brew install gdal + ## libintl.h not found? + brew install gettext + - name: Install binary units for macOS if: matrix.config.os == 'macOS-latest' run: |