edger.yaml 3.46 KB
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{
  id: edger,
  name: edgeR,
  article: "10.18129/B9.bioc.edgeR",
  website: "http://bioconductor.org/packages/release/bioc/html/edgeR.html",
  git: "git clone https://git.bioconductor.org/packages/edgeR",
  description: "Empirical Analysis of Digital Gene Expression Data.",
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  version: "3.14.0",
  documentation: "http://bioconductor.org/packages/release/bioc/manuals/edgeR/man/edgeR.pdf",
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  multiqc: "custom",
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  commands:
    [
      {
        name: edger,
        command: ~,
        output_dir: edger,
        inputs: [{ name: counts }],
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        outputs:
          [
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            { name: de_table, file: de_table.csv, description: "Tableau d'expression différentielle" },
            { name: RData, file: data.RData, description: "Sauvegarde de la session R" },
            { name: PCA, file: PCA_mqc.png, description: "PCA plot" },
            { name: Top_genes, file: Top_genes_mqc.tsv, description: "Tableau des top gènes" },
            { name: Heatmap, file: Heatmap_mqc.png, description: "Heatmap" },
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          ],
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        options:
          [
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            {
              name: edger_threads,
              prefix: -t,
              type: numeric,
              value: 4,
              min: 1,
              max: NA,
              step: 1,
              label: "Number of threads to use",
            },
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            {
              name: "edger_tx2gene",
              type: "checkbox",
              value: FALSE,
              label: "Aggregate transcripts counts to gene counts : ",
            },
            {
              name: "edger_annotations",
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              type: "input_file",
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              value: "",
              label: "Annotation file (gtf or gff) : ",
            },
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            {
              name: edger_normfact,
              type: radio,
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              value: "TMM",
              choices:
                [TMM: TMM, RLE: RLE, upperquartile: upperquartile, none: none],
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              label: "Calculate normalization factors to scale the raw library sizes.",
            },
            {
              name: "edger_dispersion",
              type: "text",
              value: "0",
              label: "Dispersion: either a numeric vector of dispersions or a character string indicating that dispersions should be taken from the data.",
            },
            {
              name: edger_testType,
              type: radio,
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              value: "exactTest",
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              choices: [exactTest: exactTest, glmLRT: glmLRT],
              label: "Test type: exactTest: Computes p-values for differential abundance for each gene between two samples, conditioning on the total count for each gene. The counts in each group are assumed to follow a binomial distribution\nglmLRT: Fits a negative binomial generalized log-linear model to the read counts for each gene and conducts genewise statistical tests.",
            },
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          ],
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      },
    ],
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  install:
    {
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      limma: ['Rscript -e ''BiocManager::install("limma", version = "3.8",Ncpus=8, clean=TRUE)'''],
      edger: ['Rscript -e ''BiocManager::install("edgeR", version = "3.8",Ncpus=8, clean=TRUE)'''],
      tximport: ['Rscript -e ''BiocManager::install("tximport", version = "3.8",Ncpus=8, clean=TRUE)'''],
      rhdf5: ['Rscript -e ''BiocManager::install("rhdf5", version = "3.8",Ncpus=8, clean=TRUE)'''],
      GenomicFeatures: ['Rscript -e ''BiocManager::install("GenomicFeatures", version = "3.8",Ncpus=8, clean=TRUE)'''],
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      pheatmap: ['Rscript -e ''install.packages("pheatmap",Ncpus=8, clean=TRUE)''']
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    },
  script: edger.script.R,
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}