{"repo":"loukesio/ggvolc","free":true,"listed":false,"github":"https://github.com/loukesio/ggvolc","clone":"git clone https://github.com/loukesio/ggvolc.git","description":"Volcano plots for differential expression in R. Reads DESeq2, edgeR and limma output directly; highlight genes of interest and compose gene tables with gt.","language":"R","stars":73,"topics":["bioinformatics","data-visualization","rna-seq","deseq2","differential-expression","genomics","ggplot2","r","rstats","volcano-plot"],"license":null,"category":"analytics","readme_excerpt":"Install the ggvolc package Install the package using the following commands How do I start? ggvolc turns the results of a differential-expression analysis — from DESeq2 , edgeR , or limma — into a clean, publication-ready volcano plot. From there you can highlight genes, auto-label the top hits, attach a gt table, or make the whole thing interactive. Start by loading the library and exploring the two example datasets that ship with the package: data(all genes) # data.frame that contains the output of differentially expressed genes head(all genes,5) # have a look at the first 5 rows # genes baseMean log2FoldChange lfcSE stat pvalue # 1 GCR1 7201.5782 2.244064 0.2004959 11.192564 4.434241e-29 # 2 OPI10 1009.4171 -2.257454 0.2096469 -10.767889 4.880607e-27 # 3 AGA2 249.1173 3.829474 0.3623263 10.569132 4.143136e-26 # 4 FIM1 1376 5237.5035 2.550409 0.2560379 9.961059 2.256459e-23 # 5 HMG1 10838.1037 2.214300 0.2229065 9.933763 2.968371e-23 # padj # 1 2.153711e-25 # 2 1.185255e-23 # 3 6.707736e-23 # 4 2.739905e-20 # 5 2.883475e-20 data(attention genes) # here is a data.frame with genes that I want to mention to the volcano plot head(attention genes,5) # have a look at the first five rows # genes baseMean log2FoldChange lfcSE stat pvalue # 1 THI13 480.5194 1.585811 0.5219706 3.038122 2.380572e-03 # 2 FBP1 22710.8428 -2.366733 0.3533032 -6.698871 2.100354e-11 # 3 TRA1 4491.1343 -1.410696 0.4384316 -3.217595 1.292700e-03 # 4 YDR222W 591.2289 -4.045918 0.9133881 -4.429572 9.442026e-06","default_branch":null,"files":null,"tree":[],"storefront":"/r/loukesio","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/loukesio/ggvolc/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."}