Update documentation

.Rbuildignore

@@ -1,3 +1,7 @@
 ^\.github$
 ^metadata\.yaml$
 ^LICENSE\.md$
+^.*\.Rproj$
+^\.Rproj\.user$
+NanoStringNorm_Example_Plots_All.pdf
+NanoStringNorm_Interactive_Plot

DESCRIPTION

@@ -2,7 +2,7 @@ Package: NanoStringNorm
 Type: Package
 Title: Normalize NanoString miRNA and mRNA Data
 Version: 3.0.0
-Date: 2025-01-17
+Date: 2025-02-07
 Authors@R: c(
 	person(c("Daryl", "M."), "Waggott", role = "aut"),
 	person("Paul", "Boutros", email = "PBoutros@mednet.ucla.edu", role = "cre"),
@@ -16,6 +16,8 @@ Suggests:
   googleVis (>= 0.2.14),
   lme4
 Description: A set of tools for normalizing, diagnostics and visualization of NanoString nCounter data.
+URL: https://github.com/uclahs-cds/package-NanoStringNorm
+BugReports: https://github.com/uclahs-cds/package-NanoStringNorm/issues
 License: GPL-2
 LazyLoad: yes
 LazyData: yes

NEWS.md

@@ -1,10 +1,11 @@
-# NanoStringNorm 3.0.0 (2025-01-17)
+# NanoStringNorm 3.0.0 (2025-02-07)
 
 ## Removed
 * Removed Excel `.xls` support due to broken CRAN dependency
 
 ## Added
 * Added CSV support for nCounter Excel files. Excel files must be converted externally.
+* Added content to README
 
 ## Changed
 * Update changelog to Markdown format

README.md

@@ -1,3 +1,74 @@
-# Nano String Norm
+# NanoStringNorm
 
-Normalize NanoString miRNA and mRNA Data
+1. [Description](#description)
+2. [Installation](#installation)
+3. [Resources](#resources)
+4. [Getting Help](#getting-help)
+5. [Citation Information](#citation-information)
+
+## Description
+
+*NanoStringNorm( is an R package for analyzing nCounter data. The nCounter platform employs direct digital detection technology that quantifies individual tagged nucleic acids without amplificaiton, enabling absolute quantification. For example plots and available functions, see the package [vignette](https://cran.r-project.org/web/packages/NanoStringNorm/vignettes/NanoStringNorm_Introduction.pdf).
+
+### Key Features
+
+* Comprehensive pre-processing for both miRNA and RNA
+* Integrated quality control and diagnostic tools
+* Flexible normalization framework with customizable methods
+* Extensive diagnostic visualization, including interactive visualization, for results interpretation
+
+
+## Installation
+
+To install the latest public release of *NanoStringNorm* from CRAN:
+
+```
+install.packages('NanoStringNorm');
+```
+
+Or to install the latest development version from GitHub:
+
+```
+# install.packages('devtools');
+
+devtools::install_github("uclahs-cds/package-NanoStringNorm");
+```
+
+
+## Resources
+
+Available resources on *NanoStringNorm* usage can be found at the package [CRAN page](https://cran.r-project.org/package=NanoStringNorm), [reference manual](https://cran.r-project.org/web/packages/NanoStringNorm/NanoStringNorm.pdf), or [vignette](https://cran.r-project.org/web/packages/NanoStringNorm/vignettes/NanoStringNorm_Introduction.pdf).
+
+
+## Getting Help
+
+Looking for guidance or support with *NanoStringNorm*? Check out our [discussions page](https://github.com/uclahs-cds/package-NanoStringNorm/discussions).
+
+Submit bugs, suggest new features, or see current work at our [issues](https://github.com/uclahs-cds/package-NanoStringNorm/issues) page.
+
+[Pull requests](https://github.com/uclahs-cds/package-NanoStringNorm/pulls) are also open for discussion.
+
+
+## Citation Information
+
+To cite *NanoStringNorm* in publications use:
+
+Waggott, D., Chu, K., Yin, S., Wouters, B.G., Liu, F.F., & Boutros, P.C. *NanoStringNorm: an extensible R package for the pre-processing of NanoString mRNA and miRNA data.* Bioinformatics 28, 11 (2012). https://doi.org/10.1093/bioinformatics/bts188
+
+### BibTeX
+
+```BibTeX
+@article{
+  NanoStringNorm,
+  title = {NanoStringNorm: An extensible R package for the pre-processing of nanostring mrna and MIRNA data},
+  journal = {Bioinformatics},
+  doi = {10.1093/bioinformatics/bts188},
+  url = {https://doi.org/10.1093/bioinformatics/bts188},
+  volume = {28},
+  number = {11},
+  year = {2012},
+  month = {April},
+  day = {17},
+  author = {Daryl Waggott and Kenneth Chu and Shaoming Yin and Bradly G. Wouters and Fei-Fei Liu and Paul C. Boutros}
+} 
+```