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# RLSeq <img src="" align="right" alt="logo" width="240" style = "border: none; float: right;"> <!-- badges: start --> [![BiocCheck](]( [![Codecov test coverage](]( [![BioC status](]( <!-- badges: end --> # Introduction *RLSeq* (part of [*RLSuite*]( is used for downstream analysis of R-loop datasets. It provides methods for data quality control and exploratory analysis within the context of the hundreds of publicly-available R-loop mapping data sets provided by [RLBase]( and accessed via [RLHub]( Finally, *RLSeq* provides a user-friendly HTML report that summarizes the analysis results. **NOTE**: To run *RLSeq* in your browser, please see [*RLBase*]( ## Installation ### From Bioconductor ```r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("RLSeq") ``` ### From Github 1. Update to the `devel` version of bioconductor. ```r BiocManager::install(version = "devel") ``` 2. Install **RLHub** and **RLSeq** with remotes. ``` r remotes::install_github("Bishop-Laboratory/RLHub") remotes::install_github("Bishop-Laboratory/RLSeq") ``` ## Quick-start This is an example workflow using a publicly-available R-loop mapping data set that was reprocessed and standardized in [*RLBase*]( ```r # Peaks and coverage can be found in RLBase rlbase <- "" pks <- file.path(rlbase, "peaks", "SRX1025890_hg38.broadPeak") cvg <- file.path(rlbase, "coverage", "") # Initialize data in the RLRanges object. # Metadata is optional, but improves the interpretability of results rlr <- RLRanges( peaks = pks, coverage = cvg, genome = "hg38", mode = "DRIP", label = "POS", sampleName = "TC32 DRIP-Seq" ) # The RLSeq command performs all analyses rlr <- RLSeq(rlr) # Generate an html report report(rlr) ``` The code above performs a typical analysis. It builds the `RLRanges` object, an extension of `GRanges` for use with RLSeq. Then, it runs all core analyses using `RLSeq()`. Finally, it generates an HTML report with `report()` (see the report [here]( ## Detail For more information, see the package website [here](