Version 1.0.1 - first try

^.github$

^README.RMD$

^NEWS.RMD$

^\.github$

*.html

# Workflow derived from https://github.com/r-lib/actions/tree/master/examples

# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help

on:

  push:

    branches: [main, master]

  pull_request:

    branches: [main, master]

name: R-CMD-check

jobs:

  R-CMD-check:

    runs-on: ${{ matrix.config.os }}

    name: ${{ matrix.config.os }} (${{ matrix.config.r }})

    strategy:

      fail-fast: false

      matrix:

        config:

          - {os: macOS-latest,   r: 'release'}

          - {os: windows-latest, r: 'release'}

          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}

          - {os: ubuntu-latest,   r: 'release'}

          - {os: ubuntu-latest,   r: 'oldrel-1'}

    env:

      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

      R_KEEP_PKG_SOURCE: yes

    steps:

      - uses: actions/checkout@v2

      - uses: r-lib/actions/setup-pandoc@v1

      - uses: r-lib/actions/setup-r@v1

        with:

          r-version: ${{ matrix.config.r }}

          http-user-agent: ${{ matrix.config.http-user-agent }}

          use-public-rspm: true

      - uses: r-lib/actions/setup-r-dependencies@v1

        with:

          extra-packages: rcmdcheck

      - uses: r-lib/actions/check-r-package@v1

      - name: Show testthat output

        if: always()

        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true

        shell: bash

      - name: Upload check results

        if: failure()

        uses: actions/upload-artifact@main

        with:

          name: ${{ runner.os }}-r${{ matrix.config.r }}-results

          path: check

Type: Package

URL: https://github.com/TobiTekath/DTUrtle, https://tobitekath.github.io/DTUrtle

Title: Differential Transcript Usage analysis of bulk and single-cell RNA-seq data

Version: 1.0.0

Version: 1.0.1

Authors@R: c(person(given = "Tobias", family = "Tekath", role = c("aut", "cre"), email = "tobias.tekath@wwu.de", comment = c(ORCID = "0000-0002-9315-5452")))

Description: Easily perform and visualize Differential Transcript Usage (DTU) analysis for bulk or single-cell RNA-seq data, utilizing transcript level quantification counts.

License: GPL (>= 3) + file LICENSE

Encoding: UTF-8

LazyData: true

Depends: R (>= 3.4.0), sparseDRIMSeq

Imports: Matrix, tximport, stageR, rtracklayer, DESeq2, GenomicFeatures, formattable, DT, Gviz, assertthat, scales, ggplot2, reshape2, BiocParallel, Matrix.utils, pheatmap, methods, GenomicRanges, GenomeInfoDb, htmltools, htmlwidgets, knitr 

Suggests: Seurat (>= 3.0.0), webshot, webshot2, magick, glmGamPoi, apeglm

Imports: 

    Matrix,

    tximport,

    stageR,

    rtracklayer,

    DESeq2,

    GenomicFeatures,

    formattable,

    DT,

    Gviz,

    assertthat,

    scales,

    ggplot2,

    reshape2,

    BiocParallel,

    Matrix.utils,

    pheatmap,

    methods,

    GenomicRanges,

    GenomeInfoDb,

    htmltools,

    htmlwidgets,

    knitr,

    lifecycle

Suggests: 

    Seurat (>= 3.0.0),

    webshot,

    webshot2,

    magick,

    glmGamPoi,

    apeglm

Remotes: github::TobiTekath/sparseDRIMSeq, bioc::BiocParallel, bioc::GenomicRanges, bioc::Gviz, bioc::rtracklayer, bioc::stageR, bioc::tximport, github::rstudio/webshot2, bioc::DESeq2, bioc::glmGamPoi, bioc::apeglm

RoxygenNote: 7.1.1

Roxygen: list(markdown = TRUE)

VignetteBuilder: knitr

RdMacros: lifecycle

BuildType: Package

PackageUseDevtools: Yes

PackageInstallArgs: --no-multiarch --with-keep.source

PackageCheckArgs: --no-vignettes --no-build-vignettes

PackageBuildArgs: --no-build-vignettes

PackageCheckArgs: --no-vignettes --ignore-vignettes