DEP
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arnesmits
DEP package
I believe there's a bug in the DEP package, as I manage to get as far as the PCA, and am able to plot individual proteins as bar plots which...
Hi there, I am attaching my code, my inputs and my results after using DEP. I do not understand how for one condition, the p value (column E of file...
How to plot heat map for average values per sample? Is it only possible to plot "contrast" or "centered"? 
Hello, I am trying to run the DEP package on a MaxQuant output for a paper ([x](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9431030/)) that used 21 different treatments on all 5 patient samples . I ran...
The downloaded binary packages are in /var/folders/n0/hj3srgsx5sd4p8_8p8_5v8wm0000gn/T//RtmpOb525A/downloaded_packages > if (!requireNamespace("BiocManager", quietly=TRUE)) + install.packages("BiocManager") > BiocManager::install("DEP") 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN:...
Hi, Thank you for this very useful tool! Is there a way to extract a specific cluster of proteins that was differentiated by k-means clustering in the heatmap?
Hi! I've been running into an issue with the test_gsea() function some weeks ago. The function aborts with the error message "EnrichR website not responding". The website itself is up...
Is there any way to substitute Spearman correlation method for the default Pearson correlation method? I can't seem to figure out which columns are being pulled from the SummarizedExperiment object...
I use test_diff to conduct Differential enrichment analysis, I had impute my data using MLE methods in advance. I found for the same protein, the p-values derived from different runs...
Fixing bug in filter_missval(): keep$rowname is vector of character strings but should be row index, hence turned to integer. Error in .SummarizedExperiment.charbound(i, rownames(x), fmt): [i,] index out of bounds: 10...
