diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 4a37e3b..7bad5af 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: @@ -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 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( 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)) 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 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" +) 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)) 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**.