User: hinkel2

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hinkel20
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Posts by hinkel2

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Comment: C: Problems with DESeq2 'design' parameter using Shiny/rhandsontable
... renderTable() (renderText() won't work because it cannot concat table to string): output$x2 <- renderTable({ values$new }) OR output$x2 <- renderTable({ values$new$experiment_name }) OR output$x2 <- renderTable({ values$new$condition }) will print o ...
written 6 weeks ago by hinkel20
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Comment: C: Problems with DESeq2 'design' parameter using Shiny/rhandsontable
... Assuming you mean DESeqDataSetFromMatrix(...) with 'dds', I printed it out using renderText(): output$x2 <- renderText({ colData(DESeqDataSetFromMatrix(countData = values$count, colData = values$new, design = ~con ...
written 6 weeks ago by hinkel20
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Comment: C: Problems with DESeq2 'design' parameter using Shiny/rhandsontable
... Hi Michael! I checked for condition column before (values$df_data) and after (values$new) user edit if it is a factor and used renderText() to get output (corresponding ui-part not shown): output$df_data <- renderText({ is.factor(values$df_data$condition) }) output$x2 <- ...
written 6 weeks ago by hinkel20
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Problems with DESeq2 'design' parameter using Shiny/rhandsontable
... Hi all! I want to create a shiny app for DESeq2 analysis. My main thought is to upload count matrix, extract colnames/experiments and provide an editable table to user in order to assign conditions to respective experiment (-> colData). After adjustment, user has to click a button in order to st ...
deseq2 shiny design rhandsontable hot_to_r() written 6 weeks ago by hinkel20 • updated 6 weeks ago by Michael Love23k
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Changes in DESeq2 Version 1.20?
... Hi all, I'm working on RNAseq data set and use DESeq2 in order to find differentially expressed genes above a given log2FoldChange, say 2 (or -2 for downregulated genes), by simply using R to filter all results above 2 and below -2, respectiely. I performed this analysis according to manual and ever ...
deseq2 written 8 months ago by hinkel20 • updated 8 months ago by Michael Love23k

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