Initialize repo

.Rbuildignore

@@ -0,0 +1,9 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.git*
+^\.idea*
+^nimbleR.iml$
+^nimbleR.*\.tar\.gz$
+^nimbleR.*\.zip$
+^\.github$
+.dockerignore

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,40 @@
+on:
+  workflow_dispatch:
+  push:
+    branches: [ main ]
+  pull_request:
+
+name: R Build and Checks
+
+jobs:
+  R-CMD-check:
+    runs-on: ubuntu-${{ matrix.config.os }}
+
+    name: ubuntu-${{ matrix.config.os }} (${{ matrix.config.r }} / ${{ matrix.config.bioc }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: 24.04, r: '4.4', bioc: '3.20' }
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: bimberlabinternal/DevOps/githubActions/r-gh-setup@master
+        with:
+          r_version: ${{ matrix.config.r }}
+          bioc_version: ${{ matrix.config.bioc }}
+          cache_version: ${{ secrets.CACHE_VERSION }}
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          args: 'c("--no-manual")'
+        env:
+          _R_CHECK_CRAN_INCOMING_: false

.gitignore

@@ -47,3 +47,7 @@ po/*~
 
 # RStudio Connect folder
 rsconnect/
+
+*.tar.gz
+*.zip
+install.bat

DESCRIPTION

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+Package: nimbleR
+Type: Package
+Title: Tools to use nimble data with seurat objects
+Version: 1.0.0
+Author: Bimber Lab
+Maintainer: The package maintainer <bimber@ohsu.edu>
+Description: An R package to format and append nimble RNA-seq count data to seurat objects.
+License: MIT
+Encoding: UTF-8
+Depends:
+    R (>= 4.3.0)
+Imports:
+    Seurat,
+    Matrix,
+    egg,
+    scales,
+    methods,
+    tidyr,
+    dplyr,
+    ggplot2
+Suggests:
+    RIRA,
+    SeuratData,
+    devtools,
+    testthat (>= 2.1.0)
+Remotes:
+    SeuratData=satijalab/seurat-data,
+    bimberlab/RIRA
+RoxygenNote: 7.3.2
+URL: https://github.com/BimberLab/nimbleR
+BugReports: https://github.com/BimberLab/nimbleR/issues

NAMESPACE

@@ -0,0 +1,8 @@
+# Generated by roxygen2: do not edit by hand
+
+export(AppendNimbleCounts)
+export(LogNormalizeUsingAlternateAssay)
+import(Seurat)
+import(dplyr)
+import(ggplot2)
+importFrom(tidyr,pivot_wider)