DEGreport
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lpantano
Create a cromphensive report of DEG list coming from any analysis of RNAseq data
Currently DEGreport depends on lasso2 which is an R4 only package. Can we have a version that is compatible with 3.6 (considering that R4 is quite broken... still...)
When I run the following code, my x-axis only shows one group instead of the 7 "times" values(stations in my case). ``` res
Can you extract as a data.frame a list of the genes included on each of the groups generated after ```degPlotCluster(res3$normalized, "condition")``` ?
Hi @lpantano , hope you're doing well! I'm seeing an error in `bcbioRNASeq::plotPCACovariates()` due to a breaking change in `DEGreport::degCovariates()`. Here's the traceback: ```r library(bcbioRNASeq) data(bcb) plotPCACovariates(bcb) > packageVersion("DEGreport") [1]...
Dear DEGreport developers, Thanks for developing this very helpful tool. I have a question regarding the DEGpattern function. In the figure below, it seems like you can sub-divided the group...
Hi Lorena I noticed that DEGplot() orders the top N genes alphabetically. I was wondering if there's an argument I can call upon to order the gene plots of N...
Hi! I am following the workflow to use degCovariates() with a DESeqDataSet object and, when I write: ``` degCovariates(counts = counts(dds), metadata = as.data.frame(colData(dds)), fdr = 0.1, scale = FALSE,...
Hi there, I am using degPatterns() from DEGreport package to do the gene clustering analysis but encounter an error message below: > Large number of genes given. Please,make sure is...
As per user request: >I am trying to use the DEGreport package to plot timecourse data using degpattern. I get really good patterns, please see attached(file attached: Summary_clusters_Group). However I...
Hi, i'm using degPatterns to cluster some genes across different time points. here is part of my code : `clusters
