User: charles.foster

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Posts by charles.foster

<prev • 6 results • page 1 of 1 • next >
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Answer: A: Using the plotting functions of clusterProfiler / enrichplot with enrichment res
... In case anyone is wondering in the future, I managed to solve the problem. The solution is a bit fiddly, but at least it works. First, load the clusterProfiler package, then read in your GOSeq enrichment results into a new data frame (in this case it's called ```results_df```). You need to format t ...
written 4 days ago by charles.foster0
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Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
... Hi all, I'm a big fan of the many plots produced by the clusterProfiler and enrichplot packages. The functions such as ```emapplot()``` require the enrichment results to have been generated using clusterProfiler (and a few other related packages, I think). However, I've carried out GO/KEGG enrichm ...
clusterprofiler enrichplot written 12 days ago by charles.foster0
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GOseq analysis with only upregulated or downregulated genes
... Dear all, I have carried out differential expression of RNA-seq data from a non-model organism using the limma+voom pipeline. Next, I wish to look for functional enrichment of DE genes using GOseq. I successfully used GOseq on my data set by following the GOseq vignette, using custom gene lengths ...
goseq written 5 weeks ago by charles.foster0 • updated 29 days ago by Nadia Davidson280
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Finding genes that are expressed only in one condition within a contrast
... Hi, I have carried out differential expression analyses comparing conditions using DESeq2. Intuitively, I have considered genes to be expressed if they have a count of at least 10 in at least some libraries (sensu Chen et al: https://f1000research.com/articles/5-1438). Hence, I carried out a filter ...
deseq2 filter written 9 weeks ago by charles.foster0 • updated 9 weeks ago by Michael Love23k
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Comment: C: Interpreting the results from lfcShrink() with apeglm in DESeq2
... Hi Michael, Great- thanks for the clarification and great program! ...
written 7 months ago by charles.foster0
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Interpreting the results from lfcShrink() with apeglm in DESeq2
... Dear all, I'm relatively new to differential expression analysis of RNA-Seq data, and I'm working my way through the DESeq2 vignette to come to terms with how it works. I'm looking to obtain a set of genes with a log2 fold change >2, and an adjusted p-value of <0.001. Following the "standard" ...
deseq2 lfcshrink apeglm written 7 months ago by charles.foster0 • updated 7 months ago by Michael Love23k

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