jhawe/rstudio_custom repository overview

FROM bioconductor/bioconductor_docker:RELEASE_3_14

[...]

RUN R -e 'BiocManager::install(\
    c("Biobase", \
      "Biostrings", \
      "M3C", \
      "kebabs", \
      "sesame", \
      "cowplot"))' \
    && rm -rf /tmp/downloaded_packages/

RUN install2.r --error \
    --deps TRUE \
        DT \
        dtplyr \
        fst \
        furrr \
        GGally \
        ggcorrplot \
        ggdendro \
        ggforce \
        ggfortify \
        ggnetwork \
        ggplotify \
        ggpubr \
        ggrepel \
        ggsci \
        ggsignif \
        ggthemes \
        gplots \
        gridExtra \
    && rm -rf /tmp/downloaded_packages/

RUN install2.r --error \
    --deps TRUE \
        janitor \
        jsonlite \
        pheatmap \
        plotly \
        survminer \
        tidyverse \
        vcfR \
        vroom \
    && rm -rf /tmp/downloaded_packages/

RUN install2.r --error \
    --deps TRUE \
        glmnet \
        glmpca \
        Hmisc \
        ggstatsplot \
        shiny \
    && rm -rf /tmp/downloaded_packages/

RUN R -e 'BiocManager::install(\
    c("BSgenome", \
      "ChIPQC", \
      "ChIPseeker", \
      "ChIPpeakAnno", \
      "clusterProfiler", \
      "ComplexHeatmap", \
      "DESeq2", \
      "GO.db", \
      "GenomicAlignments", \
      "GenomicDataCommons", \
      "GenomicRanges", \
      "JASPAR2020", \
      "MotifDb", \
      "Rsamtools", \
      "Rsubread", \
      "TFBSTools", \
      "VariantTools", \
      "ballgown", \
      "biobroom", \
      "biomaRt", \
      "edgeR", \
      "fgsea", \
      "goseq", \
      "limma", \
      "maftools", \
      "mixOmics", \
      "multtest", \
      "nanny", \
      "phenopath", \
      "rGREAT"))' \
    && rm -rf /tmp/downloaded_packages/

RUN R -e 'BiocManager::install(\
    c("recount", \
      "recount3", \
      "rhdf5", \
      "rtracklayer", \
      "seqLogo", \
      "soGGi", \
      "tidybulk", \
      "tidySummarizedExperiment", \
      "tidySingleCellExperiment", \
      "tidyHeatmap", \
      "tracktables", \
      "TxDb.Hsapiens.UCSC.hg38.knownGene", \
      "tximport"))' \
    && rm -rf /tmp/downloaded_packages/

RUN R -e 'BiocManager::install(\
    c("reticulate", "RhpcBLASctl", "BDgraph", "glasso", \
      "arrow", "susieR", "minfi", "minfiData", \
      "GOstats", "GSEABase", \
      "WGCNA", "zoo", "xgboost", \
      "randomForest", "cvTools", \
      "mixtools", "Hmisc", "qvalue"))' \
    && rm -rf /tmp/downloaded_packages/

RUN R -e 'BiocManager::install(\
    c("mashr", "MOFA2"))' \
    && rm -rf /tmp/downloaded_packages/

RUN R -e 'BiocManager::install(\
    c("mediation","coloc"))' \
    && rm -rf /tmp/downloaded_packages/