[ { "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.", "version": "3.40.0", "documentation": "http:\/\/bioconductor.org\/packages\/release\/bioc\/manuals\/edgeR\/man\/edgeR.pdf", "multiqc": "custom", "commands": [ { "name": "edger", "command": null, "category": "differential_expression", "output_dir": "edger", "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": "csv", "file": "de_table.csv", "description": "Tableau d'expression diff\u00e9rentielle" }, { "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": "Top_genes", "type": "tsv", "file": "Top_genes_mqc.tsv", "description": "Tableau des top g\u00e8nes" }, { "name": "Heatmap", "type": "png", "file": "Heatmap_mqc.png", "description": "Heatmap" } ], "options": [ { "name": "edger_threads", "prefix": "-t", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "edger_tx2gene", "type": "checkbox", "value": false, "label": "Aggregate transcripts counts to gene counts : " }, { "name": "edger_annotations", "type": "input_file", "value": "", "label": "Annotation file (gtf or gff) : " }, { "name": "edger_normfact", "type": "radio", "value": "TMM", "choices": [ { "TMM": "TMM" }, { "RLE": "RLE" }, { "upperquartile": "upperquartile" }, { "none": "none" } ], "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", "value": "exactTest", "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. glmLRT: Fits a negative binomial generalized log-linear model to the read counts for each gene and conducts genewise statistical tests." } ] } ], "install": [], "script": "edger.script.R", "citations": { "edger": [ "Robinson MD, McCarthy DJ, Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26(1), 139-140. doi: 10.1093\/bioinformatics\/btp616" ], "limma": [ "Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research, 43(7), e47. doi: 10.1093\/nar\/gkv007" ], "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: edger,\n name: edgeR,\n article: \"10.18129\/B9.bioc.edgeR\",\n website: \"http:\/\/bioconductor.org\/packages\/release\/bioc\/html\/edgeR.html\",\n git: \"git clone https:\/\/git.bioconductor.org\/packages\/edgeR\",\n description: \"Empirical Analysis of Digital Gene Expression Data.\",\n version: \"3.40.0\",\n documentation: \"http:\/\/bioconductor.org\/packages\/release\/bioc\/manuals\/edgeR\/man\/edgeR.pdf\",\n multiqc: \"custom\",\n commands:\n [\n {\n name: edger,\n command: ~,\n category: \"differential_expression\",\n output_dir: edger,\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: \"csv\", file: de_table.csv, description: \"Tableau d'expression diff\u00e9rentielle\" },\n { name: RData, type: \"RData\", file: data.RData, description: \"Sauvegarde de la session R\" },\n { name: PCA, type: \"png\", file: PCA_mqc.png, description: \"PCA plot\" },\n { name: Top_genes, type: \"tsv\", file: Top_genes_mqc.tsv, description: \"Tableau des top g\u00e8nes\" },\n { name: Heatmap, type: \"png\", file: Heatmap_mqc.png, description: \"Heatmap\" },\n ],\n options:\n [\n {\n name: edger_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: \"edger_tx2gene\",\n type: \"checkbox\",\n value: FALSE,\n label: \"Aggregate transcripts counts to gene counts : \",\n },\n {\n name: \"edger_annotations\",\n type: \"input_file\",\n value: \"\",\n label: \"Annotation file (gtf or gff) : \",\n },\n {\n name: edger_normfact,\n type: radio,\n value: \"TMM\",\n choices:\n [TMM: TMM, RLE: RLE, upperquartile: upperquartile, none: none],\n label: \"Calculate normalization factors to scale the raw library sizes.\",\n },\n {\n name: \"edger_dispersion\",\n type: \"text\",\n value: \"0\",\n label: \"Dispersion: either a numeric vector of dispersions or a character string indicating that dispersions should be taken from the data.\",\n },\n {\n name: edger_testType,\n type: radio,\n value: \"exactTest\",\n choices: [exactTest: exactTest, glmLRT: glmLRT],\n 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. glmLRT: Fits a negative binomial generalized log-linear model to the read counts for each gene and conducts genewise statistical tests.\",\n },\n ],\n },\n ],\n install:\n {\n # limma: ['Rscript -e ''BiocManager::install(\"limma\", version = \"3.13\",Ncpus=8, clean=TRUE);library(\"limma\")'''],\n # edger: ['Rscript -e ''BiocManager::install(\"edgeR\", version = \"3.13\",Ncpus=8, clean=TRUE);library(\"edgeR\")'''],\n # tximport: ['Rscript -e ''BiocManager::install(\"tximport\", version = \"3.13\",Ncpus=8, clean=TRUE);library(\"tximport\")'''],\n # rhdf5: ['Rscript -e ''BiocManager::install(\"rhdf5\", version = \"3.13,Ncpus=8, clean=TRUE);library(\"rhdf5\")'''],\n # GenomicFeatures: ['Rscript -e ''BiocManager::install(\"GenomicFeatures\", version = \"3.13\",Ncpus=8, clean=TRUE);library(\"GenomicFeatures\")'''],\n # pheatmap: ['Rscript -e ''install.packages(\"pheatmap\",Ncpus=8, clean=TRUE);library(\"pheatmap\"))''']\n },\n script: edger.script.R,\n citations: {\n edger: [\n \"Robinson MD, McCarthy DJ, Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26(1), 139-140. doi: 10.1093\/bioinformatics\/btp616\"\n ],\n limma: [\n \"Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research, 43(7), e47. doi: 10.1093\/nar\/gkv007\"\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" } ]