Merge branch 'master' of https://github.com/neurogenomics/Power_Analy…

…sis_package

.Rbuildignore

@@ -1,3 +1,25 @@
 ^poweranalysis\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
+
+Icon?
+.*\.Rproj$
+^\.Rproj\.user$
+^README.Rmd
+^\.github$
+^doc$
+^Meta$
+^codecov\.yml$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+Dockerfile
+^LICENSE\.md$
+
+node_modules$
+package-lock\.json$
+package\.json$
+^inst/markdown/.*\.html$
+^inst/markdown/test\.Rmd$
+^data-raw$
+^\.BBSoptions$

.github/workflows/rworkflows.yml

@@ -6,14 +6,14 @@ name: rworkflows
     - main
     - devel
     - RELEASE_**
-    - Rworkflows_test
+    - rworkflows_fix
   pull_request:
     branches:
     - master
     - main
     - devel
     - RELEASE_**
-    - Rworkflows_test
+    - rworkflows_fix
 jobs:
   rworkflows:
     permissions: write-all
@@ -40,14 +40,14 @@ jobs:
           cont: ~
           rspm: ~
     steps:
-    - uses: neurogenomics/rworkflows@master
+    - uses: HDash/rworkflows@force_install_packages
       with:
         run_bioccheck: ${{ false }}
         run_rcmdcheck: ${{ true }}
         as_cran: ${{ true }}
         run_vignettes: ${{ true }}
-        has_testthat: ${{ true }}
-        run_covr: ${{ true }}
+        has_testthat: ${{ false }}
+        run_covr: ${{ false }}
         run_pkgdown: ${{ true }}
         has_runit: ${{ false }}
         has_latex: ${{ false }}

.gitignore

@@ -1,2 +1,54 @@
 .Rproj.user
 inst/doc
+
+Icon?
+# R project files
+*.Rproj
+.Rproj.user
+.Ruserdata
+# History files
+.Rhistory
+.Rapp.history
+# Session Data files
+.RData
+# User-specific files
+.Ruserdata
+# .DS_Store
+# find . -name .DS_Store -print0 | xargs -0 git rm -f --ignore-unmatch
+.DS_Store
+./.DS_Store
+./**/.DS_Store
+./**/**/.DS_Store
+./**/**/**/.DS_Store
+./**/**/**/**/.DS_Store
+./**/**/**/**/**/.DS_Store
+./**/**/**/**/**/**/.DS_Store
+# Example code in package build process
+*-Ex.R
+# Output files from R CMD build
+/*.tar.gz
+# Output files from R CMD check
+/*.Rcheck/
+# RStudio files
+.Rproj.user/
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+vignettes/*.R
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+# R Environment Variables
+.Renviron
+# MotifPeeker specific
+inst/markdown/*.html
+inst/markdown/test.Rmd
+.gitignore
+codecov.yml
+!.github/codecov.yml
+docs/

DESCRIPTION

@@ -1,41 +1,47 @@
-Package: poweranalysis
-Title: Carry out Power Analysis for Differential Expression in single-cell RNA-sequencing data
-Version: 0.0.0.9000
-Authors@R: c(
-    person("Salman", "Fawad", email = "salman.fawad16@imperial.ac.uk", role = c("aut", "cre")),
-    person("Yunning", "Yuan", email = "yunning.yuan.21@ucl.ac.uk", role = c("aut")))
-Description: A pipeline for carrying out end-to-end Power Analysis for differential expression in scRNA-seq data.
-             Allows the user to carry out sum-pseudobulk DGE analysis (implemented in edgeR), which can then be used
-             as part of the main power analysis. A down-sampling approach is used, and the % of True Positive DEGs detected
-             are reported (with many layers of complexity). Other complementary analyses may also be carried out
-             using this package.
-License: MIT + file LICENSE
-Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
-Imports:
-    qs,
-    SingleCellExperiment,
-    biomaRt,
-    ggplot2,
-    cowplot,
-    viridis,
-    ggrepel,
-    edgeR,
-    stats,
-    data.table,
-    reshape2,
-    EnsDb.Hsapiens.v79,
-    grid,
-    Matrix,
-    ensembldb,
-    scales,
-    utils,
-    gtools,
-    stringr,
-    gridExtra
-Suggests: 
-    knitr,
-    rmarkdown,
-    rworkflows
-VignetteBuilder: knitr
+Type: Package
+Package: poweranalysis
+Title: Carry out Power Analysis for Differential Expression in single-cell RNA-sequencing data
+Version: 0.0.0.9000
+Authors@R: c(
+    person("Salman", "Fawad", email = "salman.fawad16@imperial.ac.uk", role = c("aut", "cre")),
+    person("Yunning", "Yuan", email = "yunning.yuan.21@ucl.ac.uk", role = c("aut")),
+    person("Hiranyamaya", "Dash", email = "hdash.work@gmail.com", role = c("ctb"),
+    comment = c(ORCID = "0009-0005-5514-505X")))
+Description: A pipeline for carrying out end-to-end Power Analysis for differential expression in scRNA-seq data.
+             Allows the user to carry out sum-pseudobulk DGE analysis (implemented in edgeR), which can then be used
+             as part of the main power analysis. A down-sampling approach is used, and the % of True Positive DEGs detected
+             are reported (with many layers of complexity). Other complementary analyses may also be carried out
+             using this package.
+License: MIT + file LICENSE
+URL: https://github.com/neurogenomics/Power_Analysis_package
+BugReports: https://github.com/neurogenomics/Power_Analysis_package/issues
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2
+Imports:
+    qs,
+    SingleCellExperiment,
+    biomaRt,
+    ggplot2,
+    cowplot,
+    viridis,
+    ggrepel,
+    edgeR,
+    stats,
+    data.table,
+    reshape2,
+    EnsDb.Hsapiens.v79,
+    grid,
+    Matrix,
+    ensembldb,
+    scales,
+    utils,
+    gtools,
+    stringr,
+    gridExtra
+Suggests: 
+    knitr,
+    rmarkdown,
+    rworkflows,
+    badger
+VignetteBuilder: knitr

README.Rmd

@@ -14,7 +14,8 @@ repo <- strsplit(URL,"/")[[1]][5]
 
 # <code>Power Analysis</code><br>Power Analysis for Differential Expression in scRNA-seq data  
 
-`r rworkflows::use_badges(add_hex = FALSE, add_authors = FALSE)`
+`r rworkflows::use_badges(add_hex = FALSE, add_authors = FALSE, add_codecov = FALSE, add_codecov_graphs = FALSE, add_license = FALSE)`
+`r badger::badge_license(license = rworkflows::get_description(refs = NULL)[[1]]$get_field("License"))`
 
 **Authors:** ***Salman Fawad, Alan Murphy, Nathan Skene***  
 **Updated:** ***`r format(Sys.Date(), '%b-%d-%Y')`***  

README.md

@@ -1,6 +1,22 @@
-# Power Analysis
 
-Wraps work from [this](https://github.com/neurogenomics/scRNA-seq_Power_Analysis) repository into an R package.
+# <code>Power Analysis</code><br>Power Analysis for Differential Expression in scRNA-seq data
+
+[![](https://img.shields.io/badge/devel%20version-0.0.0.9000-black.svg)](https://github.com/neurogenomics/Power_Analysis_package)
+[![](https://img.shields.io/github/languages/code-size/neurogenomics/Power_Analysis_package.svg)](https://github.com/neurogenomics/Power_Analysis_package)
+[![](https://img.shields.io/github/last-commit/neurogenomics/Power_Analysis_package.svg)](https://github.com/neurogenomics/Power_Analysis_package/commits/master)
+<br> [![R build
+status](https://github.com/neurogenomics/Power_Analysis_package/workflows/rworkflows/badge.svg)](https://github.com/neurogenomics/Power_Analysis_package/actions)
+<br> [![License: MIT + file
+LICENSE](https://img.shields.io/badge/license-MIT%20+%20file%20LICENSE-blue.svg)](https://cran.r-project.org/web/licenses/MIT%20+%20file%20LICENSE)
+
+**Authors:** ***Salman Fawad, Alan Murphy, Nathan Skene***  
+**Updated:** ***Oct-16-2024***
+
+## Introduction
+
+Wraps work from
+[this](https://github.com/neurogenomics/scRNA-seq_Power_Analysis)
+repository into an R package.
 
 To install (once made public), run:
 `devtools::install_github("neurogenomics/Power_Analysis")`