{"repo":"csoneson/ARMOR","free":true,"listed":false,"github":"https://github.com/csoneson/ARMOR","clone":"git clone https://github.com/csoneson/ARMOR.git","description":"Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data","language":"R","stars":168,"topics":["rna-seq","workflow"],"license":"MIT","category":"workflow-automation","readme_excerpt":"ARMOR workflow ARMOR ( A utomated R eproducible MO dular R NA-seq) is a Snakemake workflow, aimed at performing a typical RNA-seq workflow in a reproducible, automated, and partially contained manner. It is implemented such that alternative or similar analysis can be added or removed. ARMOR consists of a Snakefile , a conda environment file ( envs/environment.yaml ) a configuration file ( config.yaml ) and a set of R scripts, to perform quality control, preprocessing and differential expression analysis of RNA-seq data. The output can be combined with the iSEE R package to generate a shiny application for browsing and sharing the results. By default, the pipeline performs all the steps shown in the diagram below. However, you can turn off any combination of the light-colored steps (e.g STAR alignment or DRIMSeq analysis) in the config.yaml file. Advanced use : If you prefer other software to run one of the outlined steps (e.g. DESeq2 over edgeR , or kallisto over Salmon ), you can use the software of your preference provided you have your own script(s), and change some lines within the Snakefile . If you think your \"custom rule\" might be of use to a broader audience, let us know by opening an issue. Using the ARMOR workflow Assuming that snakemake and conda are installed (and your system has the necessary libraries to compile R packages), you can use the following commands on a test dataset: To use the ARMOR workflow on your own data, follow the steps outlined in the wiki. Wo","default_branch":null,"files":null,"tree":[],"storefront":"/r/csoneson","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/csoneson/ARMOR/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}