deseq2.yaml 4.57 KB
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{
  id: deseq2,
  name: DESeq2,
  article: "10.1186/s13059-014-0550-8",
  website: "https://bioconductor.org/packages/release/bioc/html/DESeq2.html",
  git: "git clone https://git.bioconductor.org/packages/DESeq2",
  description: "Differential gene expression analysis based on the negative binomial distribution. Using normalized count data.",
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  version: "3.8",
  documentation: "https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf",
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  multiqc: "custom",
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  commands:
    [
      {
        name: deseq2,
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        cname: "Deseq2",
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        command: ~,
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        category: "differential_expression",
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        output_dir: deseq2,
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        inputs: [{ name: counts, type: "tsv" }
                 { name: group_file, type: "popmap", file: "", description: "Path to tsv file with samples conditions"}],
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        outputs:
          [
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            { name: de_table, type: "tsv", file: de_table.csv, description: "Tableau d'expression différentielle" },
            { name: RData, type: "RData", file: data.RData, description: "Sauvegarde de la session R" },
            { name: PCA, type: "png", file: PCA_mqc.png, description: "PCA plot" },
            { name: DE_Table, type: "tsv", file: DE_Table_mqc.tsv, description: "Tableau d'expression différentielle avec p-value ajustée < 0.1" },
            { name: MA_plot, type: "png", file: MA_plot_mqc.png, description: "MA-plot log2 fold changes (on the y-axis) versus the mean of normalized counts (on the x-axis)" },
            { name: Heatmap, type: "png", file: Heatmap_mqc.png, description: "Heatmap" },
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          ],
        options:
          [
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            {
              name: deseq2_threads,
              prefix: -t,
              type: numeric,
              value: 4,
              min: 1,
              max: NA,
              step: 1,
              label: "Number of threads to use",
            },
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            {
              name: "deseq2_tx2gene",
              type: "checkbox",
              value: FALSE,
              label: "Aggregate transcripts counts to gene counts : ",
            },
            {
              name: "deseq2_annotations",
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              type: "input_file",
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              value: "",
              label: "Annotation file (gtf or gff) : ",
            },
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            # {
            #   name: deseq2_fitType,
            #   type: radio,
            #   value: "parametric",
            #   choices: [parametric: parametric, local: local, mean: mean],
            #   label: "Type of fitting of dispersions to the mean intensity",
            # },
            # {
            #   name: "deseq2_betaPrior",
            #   type: "checkbox",
            #   value: FALSE,
            #   label: "betaPrior: whether or not to put a zero-mean normal prior on the non-intercept coefficients.",
            # },
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          ],
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      },
    ],
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  install:
    {
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      latticeExtra: ['Rscript -e ''install.packages("latticeExtra",Ncpus=8, clean=TRUE);library("latticeExtra")'''],
      DESeq2: ['Rscript -e ''BiocManager::install("DESeq2", version = "3.8",Ncpus=8, clean=TRUE);library("DESeq2")'''],
      apeglm: ['Rscript -e ''BiocManager::install("apeglm", version = "3.8",Ncpus=8, clean=TRUE);library("apeglm")'''],
      BiocParallel: ['Rscript -e ''BiocManager::install("BiocParallel", version = "3.8",Ncpus=8, clean=TRUE);library("BiocParallel")'''],
      tximport: ['Rscript -e ''BiocManager::install("tximport", version = "3.8",Ncpus=8, clean=TRUE);library("tximport")'''],
      rhdf5: ['Rscript -e ''BiocManager::install("rhdf5", version = "3.8",Ncpus=8, clean=TRUE);library("rhdf5")'''],
      GenomicFeatures: ['Rscript -e ''BiocManager::install("GenomicFeatures", version = "3.8",Ncpus=8, clean=TRUE);library("GenomicFeatures")'''],
      pheatmap: ['Rscript -e ''install.packages("pheatmap",Ncpus=8, clean=TRUE);library("pheatmap")''']
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    },
  script: deseq2.script.R,
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  citations:  {
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    DESeq2: [
      "Love, M.I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15, 550 (2014). https://doi.org/10.1186/s13059-014-0550-8"
    ],
    tximport: [
      "Soneson C, Love MI, Robinson MD (2015). Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Research, 4. doi: 10.12688/f1000research.7563.1"
    ],
    GenomicFeatures: [
      "Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, et al. (2013) Software for Computing and Annotating Genomic Ranges. PLOS Computational Biology 9(8): e1003118. https://doi.org/10.1371/journal.pcbi.1003118"
    ],
    pheatmap: [
      "Kolde, R. (2012). Pheatmap: pretty heatmaps. R package version, 61, 617"
    ]
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  }
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}