SARTools - Statistical Analysis of RNA-Seq Tools

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SARTools is a R package dedicated to the differential analysis of RNA-seq data. It provides tools to generate descriptive and diagnostic graphs, to run the differential analysis with one of the well known DESeq2 or edgeR packages and to export the results into easily readable tab-delimited files. It also facilitates the generation of a HTML report which displays all the figures produced, explains the statistical methods and gives the results of the differential analysis. Note that SARTools does not intend to replace DESeq2 or edgeR: it simply provides an environment to go with them. For more details about the methodology behind DESeq2 or edgeR, the user should read their documentations and papers. SARTools is distributed with two R script templates (template_script_DESeq2.r and template_script_edgeR.r) which use functions of the package. For a more fluid analysis and to avoid possible bugs when creating the final HTML report, the user is encouraged to use them rather than writing a new script. Two other scripts are available (template_script_DESeq2_CL.r and template_script_edgeR_CL.r) to run SARTools in a shell with the Rscript command. In that case, the optparse R package must be available to interpret the command line parameters.



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