From 95d231c1a987dd19507fef7ecb7c82ab1b76fcb5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Shixiang=20Wang=20=28=E7=8E=8B=E8=AF=97=E7=BF=94=29?= Date: Tue, 20 Jan 2026 11:26:43 +0800 Subject: [PATCH] Update package title, docs, and project settings Revised the package title and description in DESCRIPTION for clarity. Improved badge formatting and code block usage in README files. Updated SigBridgeR.Rproj settings, including version, workspace, and build options. --- DESCRIPTION | 4 +- README.Rmd | 9 +++- README.md | 134 +++++++++++++++++++++++++---------------------- SigBridgeR.Rproj | 8 +-- 4 files changed, 86 insertions(+), 69 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 308ac08..acd76c8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,12 +1,12 @@ Package: SigBridgeR -Title: Multi-algorithm Integration of Phenotypic, scRNA-seq, and Bulk Data for Cell Screening +Title: Integrative Toolkit for Linking Phenotypes to Cell Subpopulations via scRNA-seq and Bulk Data Version: 3.2.0 Authors@R: c( person("Yuxi", "Yang", email = "15364051195@163.com", role = c("cre", "aut"), comment = c(ORCID = "0009-0006-1329-1224")), person("Zeyu", "Yan", email = "3191647388@qq.com", role = "ctb") ) -Description: SigBridgeR is an integrative toolkit designed to identify phenotype-associated cell subpopulations by combining phenotype(e.g. survival, drug sensitivity), bulk expression and single-cell RNA-seq data. It leverages multiple algorithms to robustly link cell features with clinical or functional phenotypes. The package provides a unified pipeline for cross-modal data analysis, enabling the discovery of biologically and clinically relevant cell states in heterogeneous samples. +Description: Identifies phenotype-associated cell subpopulations by integrating phenotypic data (e.g., survival, drug sensitivity), bulk gene expression, and single-cell RNA-seq (scRNA-seq) profiles. It employs multiple algorithms to reliably connect cellular features with clinical or functional phenotypes, offering a unified pipeline for multi-modal analysis that uncovers biologically and clinically relevant cell states in heterogeneous datasets. License: GPL (>= 3) Encoding: UTF-8 URL: https://github.com/WangLabCSU/SigBridgeR diff --git a/README.Rmd b/README.Rmd index c17c70b..f6cf786 100644 --- a/README.Rmd +++ b/README.Rmd @@ -15,7 +15,12 @@ knitr::opts_chunk$set( # **SigBridgeR** sigbridger website -[![Repo Status](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)[![License: GPL3](https://img.shields.io/badge/license-GPL3-blue.svg)](https://cran.r-project.org/web/licenses/GPL3) [![](https://img.shields.io/badge/devel%20version-3.2.0-blue.svg)](https://github.com/WangLabCSU/SigBridgeR) [![SigBridgeR status badge](https://wanglabcsu.r-universe.dev/SigBridgeR/badges/version)](https://wanglabcsu.r-universe.dev/SigBridgeR)[![R CMD check](https://github.com/WangLabCSU/SigBridgeR/workflows/R-CMD-check/badge.svg)](https://github.com/WangLabCSU/SigBridgeR/actions) [![registry status badge](https://wanglabcsu.r-universe.dev/badges/:registry)](https://wanglabcsu.r-universe.dev/) +[![Repo Status](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable) +[![License: GPL3](https://img.shields.io/badge/license-GPL3-blue.svg)](https://cran.r-project.org/web/licenses/GPL3) +[![](https://img.shields.io/badge/devel%20version-3.2.0-blue.svg)](https://github.com/WangLabCSU/SigBridgeR) +[![SigBridgeR status badge](https://wanglabcsu.r-universe.dev/SigBridgeR/badges/version)](https://wanglabcsu.r-universe.dev/SigBridgeR) +[![R CMD check](https://github.com/WangLabCSU/SigBridgeR/workflows/R-CMD-check/badge.svg)](https://github.com/WangLabCSU/SigBridgeR/actions) +[![registry status badge](https://wanglabcsu.r-universe.dev/badges/:registry)](https://wanglabcsu.r-universe.dev/) ------------------------------------------------------------------------ @@ -118,4 +123,4 @@ If you encounter problems, please check: - the [Troubleshooting Guide](vignettes/Troubleshooting.md), or - the [Github issues](https://github.com/WangLabCSU/SigBridgeR/issues) page if you want to file bug reports or feature requests -Let us know if you have ideas to make this project better! \ No newline at end of file +Let us know if you have ideas to make this project better! diff --git a/README.md b/README.md index 67c6631..f97b19d 100644 --- a/README.md +++ b/README.md @@ -1,14 +1,16 @@ + # **SigBridgeR** sigbridger website [![Repo -Status](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)[![License: +Status](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable) +[![License: GPL3](https://img.shields.io/badge/license-GPL3-blue.svg)](https://cran.r-project.org/web/licenses/GPL3) [![](https://img.shields.io/badge/devel%20version-3.2.0-blue.svg)](https://github.com/WangLabCSU/SigBridgeR) [![SigBridgeR status -badge](https://wanglabcsu.r-universe.dev/SigBridgeR/badges/version)](https://wanglabcsu.r-universe.dev/SigBridgeR)[![R -CMD +badge](https://wanglabcsu.r-universe.dev/SigBridgeR/badges/version)](https://wanglabcsu.r-universe.dev/SigBridgeR) +[![R CMD check](https://github.com/WangLabCSU/SigBridgeR/workflows/R-CMD-check/badge.svg)](https://github.com/WangLabCSU/SigBridgeR/actions) [![registry status badge](https://wanglabcsu.r-universe.dev/badges/:registry)](https://wanglabcsu.r-universe.dev/) @@ -29,86 +31,94 @@ of the latest features and bug fixes. 1. Install the development version from GitHub: - - - if (!requireNamespace("pak")) { - install.packages( - "pak", - repos = sprintf( - "https://r-lib.github.io/p/pak/stable/%s/%s/%s", - .Platform$pkgType, - R.Version()$os, - R.Version()$arch - ) - ) - } - pak::pkg_install("WangLabCSU/SigBridgeR") - -1. Install from r-universe: - - - - install.packages("SigBridgeR", repos = "https://wanglabcsu.r-universe.dev") +``` r +if (!requireNamespace("pak")) { + install.packages( + "pak", + repos = sprintf( + "https://r-lib.github.io/p/pak/stable/%s/%s/%s", + .Platform$pkgType, + R.Version()$os, + R.Version()$arch + ) + ) +} +pak::pkg_install("WangLabCSU/SigBridgeR") +``` + +2. Install from r-universe: + +``` r +install.packages("SigBridgeR", repos = "https://wanglabcsu.r-universe.dev") +``` **It is recommended to install the following packages:** For better performance: - pak::pkg_install(c( - # faster computation - "sparseMatrixStats", - "matrixStats", - "preprocessCore", - "WGCNA", - "tidyr", - "matrixTests", - "KernSmooth", - "cheapr", - # better gene symbol conversion - "scCustomize", - # parallel computation - "furrr", - "future" - )) +``` r +pak::pkg_install(c( + # faster computation + "sparseMatrixStats", + "matrixStats", + "preprocessCore", + "WGCNA", + "tidyr", + "matrixTests", + "KernSmooth", + "cheapr", + # better gene symbol conversion + "scCustomize", + # parallel computation + "furrr", + "future" +)) +``` For seamless integration with other file types such as `.h5ad` - pak::pkg_install("anndata") - # or - pak::pkg_install("anndataR") # both are supported, but anndataR is recommended +``` r +pak::pkg_install("anndata") +# or +pak::pkg_install("anndataR") # both are supported +``` For visualization: - pak::pkg_install(c( - "ggplot2", - "randomcoloR", # or RColorBrewer - "ggupset", # for upset plot - "patchwork", # for fraction stack plot - "ggforce", # for pca plot - "ggVennDiagram" # for venn diagram - )) +``` r +pak::pkg_install(c( + "ggplot2", + "randomcoloR", # or RColorBrewer + "ggupset", # for upset plot + "patchwork", # for fraction stack plot + "ggforce", # for pca plot + "ggVennDiagram" # for venn diagram +)) +``` To reproduce the tutorial to learn more usage - pak::pkg_install(c( - "zeallot", - "here", - "org.Hs.eg.db" - )) +``` r +pak::pkg_install(c( + "zeallot", + "here", + "org.Hs.eg.db" +)) +``` ## 📓 Documentation Get Started: -- [A Quick Started Guide](vignettes/Quick_Start.md) -- [Full Tutorial](vignettes/Full_Tutorial.md) for more details -- View [Github Webpage](https://wanglabcsu.github.io/SigBridgeR/) -- Use `?SigBridgeR::function_name` to access the help documents in R. +- [A Quick Started Guide](vignettes/Quick_Start.md) +- [Full Tutorial](vignettes/Full_Tutorial.md) for more details +- View [Github Webpage](https://wanglabcsu.github.io/SigBridgeR/) +- Use `?SigBridgeR::function_name` to access the help documents in R. If you encounter problems, please check: -- the [Troubleshooting Guide](vignettes/Troubleshooting.md), or -- the [Github issues](https://github.com/WangLabCSU/SigBridgeR/issues) - page if you want to file bug reports or feature requests +- the [Troubleshooting Guide](vignettes/Troubleshooting.md), or +- the [Github issues](https://github.com/WangLabCSU/SigBridgeR/issues) + page if you want to file bug reports or feature requests Let us know if you have ideas to make this project better! diff --git a/SigBridgeR.Rproj b/SigBridgeR.Rproj index 54a8759..ff46899 100644 --- a/SigBridgeR.Rproj +++ b/SigBridgeR.Rproj @@ -1,8 +1,7 @@ -Version: 3.2.0 -ProjectId: 0d1fb75d-343f-4a9e-9406-b3114691357f +Version: 1.0 RestoreWorkspace: Default -SaveWorkspace: Ask +SaveWorkspace: Default AlwaysSaveHistory: Default EnableCodeIndexing: Yes @@ -13,6 +12,9 @@ Encoding: UTF-8 RnwWeave: Sweave LaTeX: pdfLaTeX +AutoAppendNewline: Yes + BuildType: Package PackageUseDevtools: Yes PackageInstallArgs: --no-multiarch --with-keep.source +PackageRoxygenize: rd,collate,namespace