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Recent Replies
Comment: ClusterProfiler enrichKEGG – remove organism name in plots?
by
jv
★
1.0k
Just giving OP some options since they didn't show their code. In my case I am using `clusterProfiler::download_KEGG` to download KEGG gene…
Comment: Time change in expression vs time change in phenotype
by
Ivan
•
0
Worst case we could use DEseq2 to associate (E_t2 - E_t1) with I(t), where I(t) is an indicator variable, =1 at t1 and =2 at t2… So now we …
Comment: activity of unloaded/unassembled Tn5
by
ATpoint
70k
Appreciate your efforts but this is all off-topic here. Suggest to put this in a GitHub Pages or similar location to make it accessable for…
Comment: Nextflow rnaseq finishing early
by
ATpoint
70k
Regardless, you can ask this at nf-core slack which has a dedicated channel for this pipeline.
https://nf-co.re/join/slack => channel…
Comment: Nextflow rnaseq finishing early
by
ATpoint
70k
Be nice to people...you have the problem and lack expertise to solve it, not the people trying to help you.
Answer: activity of unloaded/unassembled Tn5
by
callumjcparr
•
0
![enter image description here][1]
Example of TapeStation of scaled-up reaction in 500,000 nuclei. Working on the assumption we usually …
Comment: Nextflow rnaseq finishing early
by
Raygozak
★
1.4k
You're asking me? why do you think i'm here asking if i hadn't checked everything else?
Comment: Nextflow rnaseq finishing early
by
Ram
38k
> the RNA-seq pipeline from nextflow
**which** RNA-seq pipeline? Can you add a link to it please?
Comment: Nextflow rnaseq finishing early
by
Pierre Lindenbaum
153k
is there any step that depends of the QC ? eg: MULTIQC_TSV_FAIL_TRIMMED or MULTIQC .
what happens if any QC fails ?
Answer: ClusterProfiler enrichKEGG – remove organism name in plots?
by
e.r.zakiev
▴
30
before invoking `dotplot` function replace the parts of the strings in your `enrichKEGG` result (let's call it `ekegg`):
`ekegg@result$D…
Comment: syntax errors when running part3 all-against-all
by
Ram
38k
What on earth are you talking about? Please add some context, we are not mind readers.
Answer: differential gene analysis
by
ATpoint
70k
It is impossible to tell anything about these plots as code is missing. As said already, standard tests such as t-tests and Wilcox tests ar…
Comment: ClusterProfiler enrichKEGG – remove organism name in plots?
by
e.r.zakiev
▴
30
When using `enrichKEGG` function with the default parameters (`ekegg <- enrichKEGG(gene = ENTREZID_genes, organism = 'mmu', pvalueCutoff = …
Comment: differential gene analysis
by
kalyani
•
0
i have used DESeq2 but same issue.
if u have a reference for these please share.
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