ingmbioinfo · federicomarini · Feb 10, 2026 · Feb 10, 2026 · Feb 10, 2026 · Feb 10, 2026
diff --git 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:
@@ -146,10 +146,8 @@ 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
+          ## libintl.h not found?
+          brew install gettext
 
       - name: Install binary units for macOS
         if: matrix.config.os == 'macOS-latest'

diff --git 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(

diff --git 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))

diff --git 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 <https://doi.org/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
@@ -50,37 +50,52 @@ integration into existing workflows.
 - **Python docs**:
   `CIA Python documentation <https://cia-python.readthedocs.io/en/latest/index.html>`\_
 - **R Package and Tutorial**:
-  `CIA R GitHub Repository <https://github.com/ingmbioinfo/CIA_R>`\_
+  `CIA R GitHub Repository <https://github.com/ingmbioinfo/cia/tree/master/tutorial>`\_
 
 ## 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). <doi:10.1186/s12859-025-06320-z>
+> <https://doi.org/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

diff --git a/inst/CITATION 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"
+)
diff --git a/man/load_signatures.Rd b/man/load_signatures.Rd
diff --git 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 <https://doi.org/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**.