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Fig. 3 | BMC Bioinformatics

Fig. 3

From: BEAVR: a browser-based tool for the exploration and visualization of RNA-seq data

Fig. 3

DGE table output from a typical use case for BEAVR. a Once DGE analysis completes in BEAVR, an interactive table is shown in the Gene Table tab. This table provides users with log2 fold change (LFC) values for each gene as well as p values and adjusted p values (padj). Users can search for a particular gene of interest by its gene name or sort the table based on the contents of any column. A copy of the table can be saved using the download button in the sidebar. The data shown here is the output of DGE analysis performed on the Sehrawat et al. dataset. ‘DMSO’ was selected as the control condition and ‘SP2509’ was selected as the treatment condition in the Settings tab. The false discovery rate (FDR) was set to 10% and genes with less than 10 reads were dropped from analysis. b The DGE results table in the Gene Table tab can be filtered by any metric using the controls provided in the sidebar. The available filtering options are min/max LFC, min/max p value, min/max padj, min/max baseMean (normalized mean), min/max lfcSE (LFC standard error) and min/max stat (test statistic). The filtered table can be downloaded using the download button in the sidebar. If filtering is enabled, the filtered table will be used to generate the volcano plot in the Volcano Plot tab

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