## ----eval=FALSE--------------------------------------------------------------- # library(phantasus) # servePhantasus() ## ---- out.width = "750px", echo = FALSE--------------------------------------- knitr::include_graphics("images/start_screen.jpg") ## ---- out.width = "750px", echo = FALSE--------------------------------------- knitr::include_graphics("images/dataset_loaded.jpg") ## ---- out.width = "500px", echo = FALSE--------------------------------------- knitr::include_graphics("images/huge_value.jpg") ## ---- out.width = "500px", echo = FALSE--------------------------------------- knitr::include_graphics("images/adjust_tool.jpg") ## ---- out.width = "600px", echo = FALSE--------------------------------------- knitr::include_graphics("images/duplicates.jpg") ## ---- out.width = "500px", echo = FALSE--------------------------------------- knitr::include_graphics("images/collapse_tool.jpg") ## ---- out.width = "500px", echo = FALSE--------------------------------------- knitr::include_graphics("images/calculated_annotation_tool.jpg") ## ---- out.width = "600px", echo = FALSE--------------------------------------- knitr::include_graphics("images/calculated_annotation_loaded.jpg") ## ---- out.width = "500px", echo = FALSE--------------------------------------- knitr::include_graphics("images/filter_tool.jpg") ## ---- out.width = "500px", echo = FALSE--------------------------------------- knitr::include_graphics("images/filter_tool_result.jpg") ## ---- out.width = "550px", echo = FALSE--------------------------------------- knitr::include_graphics("images/pcaplot_tool_clean.png") ## ---- out.width = "550px", echo = FALSE--------------------------------------- knitr::include_graphics("images/pcaplot_tool_finished.png") ## ---- out.width = "500px", echo = FALSE--------------------------------------- knitr::include_graphics("images/kmeans_tool.jpg") ## ---- out.width = "600px", echo = FALSE--------------------------------------- knitr::include_graphics("images/kmeans_result.jpg") ## ---- out.width = "500px", echo = FALSE--------------------------------------- knitr::include_graphics("images/hierarchical_tool.jpg") ## ---- out.width = "600px", echo = FALSE--------------------------------------- knitr::include_graphics("images/good_samples.jpg") ## ---- out.width = "500px", echo = FALSE--------------------------------------- knitr::include_graphics("images/limma_tool.jpg") ## ---- out.width = "600px", echo = FALSE--------------------------------------- knitr::include_graphics("images/limma_results.png") ## ---- out.width = "600px", echo = FALSE--------------------------------------- knitr::include_graphics("images/fgsea_tool.png") ## ---- out.width = "800px", echo = FALSE--------------------------------------- knitr::include_graphics("images/fgsea_result.png") ## ---- out.width = "600px", echo = FALSE--------------------------------------- knitr::include_graphics("images/annotation_tool.png") ## ---- out.width = "600px", echo = FALSE--------------------------------------- knitr::include_graphics("images/annotation_result.png") ## ---- out.width = "600px", echo = FALSE--------------------------------------- knitr::include_graphics("images/enrichr.png") ## ---- out.width = "600px", echo = FALSE--------------------------------------- knitr::include_graphics("images/enrichr_result.png") ## ---- out.width = "300px", echo = FALSE--------------------------------------- knitr::include_graphics("images/shiny_gam.jpg") ## ---- out.width = "600px", echo = FALSE--------------------------------------- knitr::include_graphics("images/shiny_gam_result.jpg") ## ---- out.width = "600px", echo = FALSE--------------------------------------- knitr::include_graphics("images/fgsea_genes.png") ## ---- out.width = "600px", echo = FALSE--------------------------------------- knitr::include_graphics("images/fgsea_search.png") ## ---- out.width = "600px", echo = FALSE--------------------------------------- knitr::include_graphics("images/GSEA_plot.png") ## ---- out.width = "600px", echo = FALSE--------------------------------------- knitr::include_graphics("images/link.png") ## ---- out.width="500px", echo = FALSE----------------------------------------- knitr::include_graphics("images/open_file_tool.jpg") ## ---- message=FALSE, cache=TRUE, eval=FALSE----------------------------------- # library(GEOquery) # library(limma) # gse14308 <- getGEO("GSE14308", AnnotGPL = TRUE)[[1]] # gse14308$condition <- sub("-.*$", "", gse14308$title) # pData(gse14308) <- pData(gse14308)[, c("title", "geo_accession", "condition")] # gse14308 <- gse14308[, order(gse14308$condition)] # # fData(gse14308) <- fData(gse14308)[, c("Gene ID", "Gene symbol")] # exprs(gse14308) <- normalizeBetweenArrays(log2(exprs(gse14308)+1), method="quantile") # # ess <- list(GSE14308_norm=gse14308) # # preloadedDir <- tempdir() # # save(ess, file=file.path(preloadedDir, "GSE14308_norm.rda")) ## ---- eval=F------------------------------------------------------------------ # servePhantasus(preloadedDir=preloadedDir) ## ---- out.width="650px", echo = FALSE----------------------------------------- knitr::include_graphics("images/gse14308_norm.png") ## ---- eval=F------------------------------------------------------------------ # updateARCHS4(cacheDir=cacheDir) ## ---- eval=TRUE--------------------------------------------------------------- data("fgseaExample", package="phantasus") head(fgseaExample)