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ViDGER <img src="man/figures/logo-02.svg" align="right" height="120"/> ====================================================================== [![Build Status](]( [![codecov](]( [![bioc](]( [![platforms](]( Overview -------- ViDGER (**Vi**sualization of **D**ifferential **G**ene **E**xpression using **R**), is an `R` package that can rapidly generate information-rich visualizations for the interpretation of differential gene expression results from three widely-used tools: `Cuffdiff`, `DESeq2`, and `edgeR`. Installation ------------ The stable version of this package is available on [Bioconductor]( . You can install it by: ``` r if (!require("BiocManager")) install.packages("BiocManager") BiocManager::install("vidger") ``` If you want the latest version, install it directly from this GitHub repo: ``` r if (!require("devtools")) install.packages("devtools") devtools::install_github("btmonier/vidger", ref = "devel") ``` Functions --------- The stable release of `vidger` has 9 visualization functions: - `vsScatterPlot()` - `vsScatterMatrix()` - `vsBoxplot()` - `vsDEGMatrix()` - `vsVolcano()` - `vsVolcanoMatrix()` - `vsMAPlot()` - `vsMAMatrix()` - `vsFourWay()` Loading test data ----------------- To simulate the usage of the three aformentioned tools, "toy" data sets have been implemented in this package. Each of these data sets represents their respective `R` class: - `df.cuff` A `cuffdiff` output file. - `df.deseq` A `DESeq2` object class. - `df.edger` An `edgeR` object class. To load these data sets, use the following command: ``` r data("<object-type>") ``` ...where `"<object-type>"` is one of the previously mentioned data sets. Getting help ------------ For additional information on these functions, please see the given documentation in the `vidger` package by adding the `?` help operator before any of the given functions in this package or by using the `help()` function. For a more in-depth analysis, consider reading the vignette provided with this package: ``` r vignette("vidger") ``` ------------------------------------------------------------------------ *Last updated:* 2019-01-18