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$set(
# **SigBridgeR** 
-[](https://lifecycle.r-lib.org/articles/stages.html#stable)[](https://cran.r-project.org/web/licenses/GPL3) [](https://github.com/WangLabCSU/SigBridgeR) [](https://wanglabcsu.r-universe.dev/SigBridgeR)[](https://github.com/WangLabCSU/SigBridgeR/actions) [](https://wanglabcsu.r-universe.dev/)
+[](https://lifecycle.r-lib.org/articles/stages.html#stable)
+[](https://cran.r-project.org/web/licenses/GPL3)
+[](https://github.com/WangLabCSU/SigBridgeR)
+[](https://wanglabcsu.r-universe.dev/SigBridgeR)
+[](https://github.com/WangLabCSU/SigBridgeR/actions)
+[](https://wanglabcsu.r-universe.dev/)
------------------------------------------------------------------------
@@ -118,4 +123,4 @@ If you encounter problems, please check:
- the [Troubleshooting Guide](vignettes/Troubleshooting.md), or
- the [Github issues](https://github.com/WangLabCSU/SigBridgeR/issues) page if you want to file bug reports or feature requests
-Let us know if you have ideas to make this project better!
\ No newline at end of file
+Let us know if you have ideas to make this project better!
diff --git a/README.md b/README.md
index 67c6631..f97b19d 100644
--- a/README.md
+++ b/README.md
@@ -1,14 +1,16 @@
+
# **SigBridgeR**
[](https://lifecycle.r-lib.org/articles/stages.html#stable)[](https://lifecycle.r-lib.org/articles/stages.html#stable)
+[](https://cran.r-project.org/web/licenses/GPL3)
[](https://github.com/WangLabCSU/SigBridgeR)
[](https://wanglabcsu.r-universe.dev/SigBridgeR)[](https://wanglabcsu.r-universe.dev/SigBridgeR)
+[](https://github.com/WangLabCSU/SigBridgeR/actions)
[](https://wanglabcsu.r-universe.dev/)
@@ -29,86 +31,94 @@ of the latest features and bug fixes.
1. Install the development version from GitHub:
-
-
- if (!requireNamespace("pak")) {
- install.packages(
- "pak",
- repos = sprintf(
- "https://r-lib.github.io/p/pak/stable/%s/%s/%s",
- .Platform$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