[ { "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.", "version": "1.38", "documentation": "https:\/\/bioconductor.org\/packages\/release\/bioc\/manuals\/DESeq2\/man\/DESeq2.pdf", "multiqc": "custom", "commands": [ { "name": "deseq2", "cname": "Deseq2", "command": null, "category": "differential_expression", "output_dir": "deseq2", "inputs": [ { "name": "counts", "type": "tsv", "expand": true }, { "name": "popmap_file", "type": "popmap", "file": "", "description": "Path to tsv file with samples conditions" } ], "outputs": [ { "name": "de_table", "type": "tsv", "file": "de_table.csv", "description": "Tableau d'expression diff\u00e9rentielle" }, { "name": "raw_counts", "type": "tsv", "file": "raw_counts.tsv", "description": "Sauvegarde de la matrice des comptes non normalis\u00e9s" }, { "name": "PCA", "type": "png", "file": "PCA_mqc.png", "description": "PCA plot" }, { "name": "Top_genes", "type": "tsv", "file": "Top_genes_mqc.yaml", "description": "Tableau d'expression diff\u00e9rentielle avec p-value ajust\u00e9e < 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" } ], "options": [ { "name": "deseq2_threads", "prefix": "-t", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "deseq2_tx2gene", "type": "checkbox", "value": false, "label": "Aggregate transcripts counts to gene counts : " }, { "name": "deseq2_annotations", "type": "input_file", "value": "", "label": "Annotation file (gtf or gff) : " }, { "name": "deseq2_biomaRtDataset", "type": "select", "choices": [ { "None": "None" }, { "Mus musculus": "mus_musculus" }, { "Homo sapiens": "homo_sapiens" }, { "Nile tilapia": "oreochromis_niloticus" }, { "Drosophila melanogaster": "drosophila_melanogaster" } ], "value": "None", "label": "Species name in Ensembl.org" }, { "name": "deseq2_minpvalue", "prefix": "-pvalue", "type": "numeric", "value": 0.05, "min": 0.0001, "max": "NA", "step": 0.0001, "label": "Filter for Adjusted p-values <= to :" }, { "name": "deseq2_topGenes", "prefix": "-topG", "type": "numeric", "value": 40, "min": 10, "max": 100, "step": 1, "label": "Number of top Genes (based on p-values) to show in the report" } ] } ], "install": [], "script": "deseq2.script.R", "citations": { "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, Pag\u00e8s 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" ] }, "yaml": "{\n id: deseq2,\n name: DESeq2,\n article: \"10.1186\/s13059-014-0550-8\",\n website: \"https:\/\/bioconductor.org\/packages\/release\/bioc\/html\/DESeq2.html\",\n git: \"git clone https:\/\/git.bioconductor.org\/packages\/DESeq2\",\n description: \"Differential gene expression analysis based on the negative binomial distribution. Using normalized count data.\",\n version: \"1.38\",\n documentation: \"https:\/\/bioconductor.org\/packages\/release\/bioc\/manuals\/DESeq2\/man\/DESeq2.pdf\",\n multiqc: \"custom\",\n commands:\n [\n {\n name: deseq2,\n cname: \"Deseq2\",\n command: ~,\n category: \"differential_expression\",\n output_dir: deseq2,\n inputs: \n [\n { name: counts, type: \"tsv\", expand: true }, #will expand over counts for samples in SAMPLES\n { name: popmap_file, type: \"popmap\", file: \"\", description: \"Path to tsv file with samples conditions\"},\n ],\n outputs:\n [\n { name: de_table, type: \"tsv\", file: de_table.csv, description: \"Tableau d'expression diff\u00e9rentielle\" },\n { name: raw_counts, type: \"tsv\", file: raw_counts.tsv, description: \"Sauvegarde de la matrice des comptes non normalis\u00e9s\" },\n { name: PCA, type: \"png\", file: PCA_mqc.png, description: \"PCA plot\" },\n { name: Top_genes, type: \"tsv\", file: Top_genes_mqc.yaml, description: \"Tableau d'expression diff\u00e9rentielle avec p-value ajust\u00e9e < 0.1\" },\n { 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)\" },\n { name: Heatmap, type: \"png\", file: Heatmap_mqc.png, description: \"Heatmap\" },\n ],\n options:\n [\n {\n name: deseq2_threads,\n prefix: -t,\n type: numeric,\n value: 4,\n min: 1,\n max: NA,\n step: 1,\n label: \"Number of threads to use\",\n },\n {\n name: \"deseq2_tx2gene\",\n type: \"checkbox\",\n value: FALSE,\n label: \"Aggregate transcripts counts to gene counts : \",\n },\n {\n name: \"deseq2_annotations\",\n type: \"input_file\",\n value: \"\",\n label: \"Annotation file (gtf or gff) : \",\n },\n {\n name: \"deseq2_biomaRtDataset\",\n type: select,\n choices: [\n None: \"None\",\n Mus musculus: \"mus_musculus\",\n Homo sapiens: \"homo_sapiens\",\n Nile tilapia: \"oreochromis_niloticus\",\n Drosophila melanogaster: \"drosophila_melanogaster\"\n ],\n value: \"None\",\n label: \"Species name in Ensembl.org\"\n },\n {\n name: deseq2_minpvalue,\n prefix: \"-pvalue\",\n type: numeric,\n value: 0.05,\n min: 0.0001,\n max: NA,\n step: 0.0001,\n label: \"Filter for Adjusted p-values <= to :\",\n },\n {\n name: deseq2_topGenes,\n prefix: -topG,\n type: numeric,\n value: 40,\n min: 10,\n max: 100,\n step: 1,\n label: \"Number of top Genes (based on p-values) to show in the report\",\n },\n # {\n # name: deseq2_fitType,\n # type: radio,\n # value: \"parametric\",\n # choices: [parametric: parametric, local: local, mean: mean],\n # label: \"Type of fitting of dispersions to the mean intensity\",\n # },\n # {\n # name: \"deseq2_betaPrior\",\n # type: \"checkbox\",\n # value: FALSE,\n # label: \"betaPrior: whether or not to put a zero-mean normal prior on the non-intercept coefficients.\",\n # },\n ],\n },\n ],\n install:\n {\n # latticeExtra: ['Rscript -e ''install.packages(\"latticeExtra\",Ncpus=8, clean=TRUE);library(\"latticeExtra\")'''],\n # DESeq2: ['Rscript -e ''BiocManager::install(\"DESeq2\", version = \"3.14\",Ncpus=8, clean=TRUE);library(\"DESeq2\")'''],\n # apeglm: ['Rscript -e ''BiocManager::install(\"apeglm\", version = \"3.14\",Ncpus=8, clean=TRUE);library(\"apeglm\")'''],\n # BiocParallel: ['Rscript -e ''BiocManager::install(\"BiocParallel\", version = \"3.14\",Ncpus=8, clean=TRUE);library(\"BiocParallel\")'''],\n # tximport: ['Rscript -e ''BiocManager::install(\"tximport\", version = \"3.14\",Ncpus=8, clean=TRUE);library(\"tximport\")'''],\n # rhdf5: ['Rscript -e ''BiocManager::install(\"rhdf5\", version = \"3.14\",Ncpus=8, clean=TRUE);library(\"rhdf5\")'''],\n # GenomicFeatures: ['Rscript -e ''BiocManager::install(\"GenomicFeatures\", version = \"3.14\",Ncpus=8, clean=TRUE);library(\"GenomicFeatures\")'''],\n # pheatmap: ['Rscript -e ''install.packages(\"pheatmap\",Ncpus=8, clean=TRUE);library(\"pheatmap\")'''],\n # certificates: [apt-get install -y ca-certificates]\n },\n script: deseq2.script.R,\n citations: {\n DESeq2: [\n \"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\"\n ],\n tximport: [\n \"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\"\n ],\n GenomicFeatures: [\n \"Lawrence M, Huber W, Pag\u00e8s 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\"\n ],\n pheatmap: [\n \"Kolde, R. (2012). Pheatmap: pretty heatmaps. R package version, 61, 617\"\n ]\n }\n}\n" } ]