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User: unamourdeswann

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2 months ago
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1 year, 12 months ago
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m****************@inra.fr

Posts by unamourdeswann

<prev • 7 results • page 1 of 1 • next >
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Answer: A: compareCluster on Mus musculus
... D'oh! Using: compareCluster(geneCluster=list("1"=l), fun="enrichKEGG", organism="mmu", pvalueCutoff=0.05, pAdjustMethod="BH")` works perfectly fine (geneCluster obviously expects a list of genes). Sorry to everyone! ...
written 8 weeks ago by unamourdeswann10
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compareCluster on Mus musculus
... Hello everyone. I probably mistyped something, but I cannot use compareCluster on my data (Mouse mm10). Here is a minimal example (using R --vanilla): library(clusterProfiler) [...] l <- c("14654", "224897", "56463", "53623", "57875", "22245", "54610", "224997", "15162", "26438", "76889", " ...
clusterprofiler written 8 weeks ago by unamourdeswann10
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Comment: C: Split GRanges to GRangeList based on mcols value
... Cool! Did not know either. ...
written 3 months ago by unamourdeswann10
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Comment: C: Split GRanges to GRangeList based on mcols value
... I did know `split`, but only in combination with another GRL (or seqnames). Glad to know `split` + `~`, thanks! ...
written 3 months ago by unamourdeswann10
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Split GRanges to GRangeList based on mcols value
... I have a GRanges with a factor in mcols gr <- GRanges(seqnames = c("1", "2"), IRanges(start=c(1000, 2000), width=100), strand = c("+", "+"), category = c("A", "B")) I would like to split gr based on category, in order to have a GRangesList that would be similar to: grl <- GRangesList(A=gr[1], ...
granges written 3 months ago by unamourdeswann10 • updated 3 months ago by Michael Lawrence10k
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Comment: C: results function of DESeq2 devel fails
... Thanks a lot! I will wait for their fix. (BTW: BioConductor recommends that seq_len() or seq_along() be used instead of 1:... :-) ...
written 13 months ago by unamourdeswann10
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results function of DESeq2 devel fails
... I tried to follow the DESeq2 tutorial, and ended up with a error. library("pasilla") library("DESeq2") pasCts <- system.file("extdata", "pasilla_gene_counts.tsv", package="pasilla", mustWork=TRUE) pasAnno <- system.file("extdata", "pasilla_sample_annotation.csv", package="pasilla", mustWork=TR ...
deseq2 written 13 months ago by unamourdeswann10

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