Update package title, docs, and project settings

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

README.Rmd

@@ -15,7 +15,12 @@ knitr::opts_chunk$set(
 
 # **SigBridgeR** <a href="https://wanglabcsu.github.io/SigBridgeR/"><img src="man/figures/logo_white.png" alt="sigbridger website" align="right" height="139"/></a>
 
-[![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!
+Let us know if you have ideas to make this project better!

README.md

@@ -1,14 +1,16 @@
+
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 # **SigBridgeR** <a href="https://wanglabcsu.github.io/SigBridgeR/"><img src="man/figures/logo_white.png" alt="sigbridger website" align="right" height="139"/></a>
 
 [![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!

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