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• W2951093721 abstract "Abstract The extensive generation of RNA sequencing (RNA-seq) data in the last decade has resulted in a myriad of specialized software for its analysis. Each software module typically targets a specific step within the analysis pipeline, making it necessary to join several of them to get a single cohesive workflow. Multiple software programs automating this procedure have been proposed, but often lack modularity, transparency or flexibility. We present ARMOR, which performs an end-to-end RNA-seq data analysis, from raw read files, via quality checks, alignment and quantification, to differential expression testing, geneset analysis and browser-based exploration of the data. ARMOR is implemented using the Snakemake workflow management system and leverages conda environments; Bioconductor objects are generated to facilitate downstream analysis, ensuring seamless integration with many R packages. The workflow is easily implemented by cloning the GitHub repository, replacing the supplied input and reference files and editing a configuration file. Although we have selected the tools currently included in ARMOR, the setup is modular and alternative tools can be easily integrated." @default.
• W2951093721 created "2019-06-27" @default.
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• W2951093721 date "2019-03-12" @default.
• W2951093721 modified "2023-10-03" @default.
• W2951093721 title "ARMOR: an Automated Reproducible MOdular workflow for preprocessing and differential analysis of RNA-seq data" @default.
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• W2951093721 doi "https://doi.org/10.1101/575951" @default.
• W2951093721 hasPublicationYear "2019" @default.
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