Eccb2024

.github/workflows/rworkflows.yml

@@ -0,0 +1,57 @@
+name: rworkflows
+'on':
+  push:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+  pull_request:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+jobs:
+  rworkflows:
+    permissions: write-all
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    strategy:
+      fail-fast: ${{ false }}
+      matrix:
+        config:
+        - os: ubuntu-latest
+          bioc: devel
+          r: auto
+          cont: ghcr.io/bioconductor/bioconductor_docker:devel
+          rspm: ~
+        - os: macOS-latest
+          bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+        - os: windows-latest
+          bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+    steps:
+    - uses: neurogenomics/rworkflows@master
+      with:
+        run_bioccheck: ${{ false }}
+        run_rcmdcheck: ${{ true }}
+        as_cran: ${{ true }}
+        run_vignettes: ${{ true }}
+        has_testthat: ${{ true }}
+        run_covr: ${{ true }}
+        run_pkgdown: ${{ true }}
+        has_runit: ${{ false }}
+        has_latex: ${{ false }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run_docker: ${{ false }}
+        DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
+        runner_os: ${{ runner.os }}
+        cache_version: cache-v1
+        docker_registry: ghcr.io

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tidyomicsWorkshop
 Title: Tidy genomic and transcriptomic analyses 
-Version: 0.16.3
+Version: 0.17.0
 Authors@R: 
     c(
     person(given = "Stefano",
@@ -14,8 +14,7 @@ Authors@R:
            email = "michaelisaiahlove@gmail.com",
            comment = c(ORCID = "0000-0001-8401-0545"))
 	   )
-Description: Workflow for BioC conference showing tidy genomic
-    and transcriptomic analyses.
+Description: Workshop material for tidyomics, including transcriptomics and genomics.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
@@ -28,10 +27,16 @@ Depends:
 Imports:
     SummarizedExperiment, 
     SingleCellExperiment,
+    SeuratObject,
+    Seurat,
     tidySummarizedExperiment,
     tidySingleCellExperiment,
     tidygate,
     tidyseurat,
+    SpatialExperiment,
+    tidySpatialExperiment,
+    plyranges,
+    nullranges,
     stats,
     utils,
     tibble,
@@ -42,23 +47,30 @@ Imports:
     tidyr,
     purrr,
     forcats,
-    ggrepel,
-    plotly,
-    igraph,
-    broom,
     devtools,
     rlang,
     magrittr,
     R.utils,
+Suggests:
+    knitr,
+    rmarkdown,
+    pkgdown,
+    STexampleData,
     dittoSeq,
     tidybulk,
     glue,
     scater,
-    batchelor
-Suggests:
-    knitr,
-    rmarkdown,
-    pkgdown
+    scran,
+    batchelor,
+    ggrepel,
+    plotly,
+    igraph,
+    broom,
+    ggspavis
+Remotes:
+    satijalab/seurat-wrappers,
+    stemangiola/tidySingleCellExperiment,
+    william-hutchison/tidySpatialExperiment
 Biarch: true
 URL: https://tidy-biology.github.io/TidyGenomicsTranscriptomicsWorkshop
 BugReports: https://github.com/tidy-biology/TidyGenomicsTranscriptomicsWorkshop/issues/new/choose

NAMESPACE

@@ -1,2 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+import(SeuratObject)
+importFrom(SingleCellExperiment,SingleCellExperiment)
+importFrom(SummarizedExperiment,SummarizedExperiment)
+importFrom(ggplot2,theme)