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Hi all,
I am analysing 16S MiSeq data from 3 separate runs for the same project. The 3rd MiSeq run had a higher sequencing depth. Partly for this reason, I observe a significant batch effect, where…
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Dear Liz,
I ran SQANTI2 on a dataset and I would like to ask for your help to understand some of the output plots.
I do not see why % transcripts in the "Isoform distribution across structural c…
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I have a similar geometry as given in blunted_cone tutorial.
Mesh check was fine. No errors generated.
But while running hy2Foam command I encountered errors attached.
P.S - The example file ran fi…
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Hey @IslaMS ,
I have just written up the meeting notes here, if you want to have a look:
https://github.com/DaniGargya/dissertation/blob/master/notes/200306_meeting_Isla.docx
Did you manage to …
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Hi _all_
I've an issue with the phyloseq_mult_raref_avg function; it works on this phyloseq object.
phyloseq_summary(ps, cols = NULL, more_stats = FALSE,
+ lo…
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Hello,
I'm wondering if I could use this package to generate a "rarefaction" curve for libraries of sRNA-seq,
Cheers,
Luis Alfonso.
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The analysis of the IBR is limited to the site with the smallest number of individuals. One site (NODI) has only 6 individuals which means that the scale for the IBR is quite limited. If we drop NODI …
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Hi,
For several plotting functions I would like to merge my samples into my three clinical groups. Each sample is adjusted to even sequencing depth, so this is not a problem for merge_samples. However…
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I try to rarefied my data with `subsample_count` but it send me an error that the table is normalised although I set the normalization to None.
```
biom = ca.read_amplicon("table.biom" ,sample_met…
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There is an unknown error originating from https://groups.google.com/d/msg/poppr/F-HImtnMrA8/mp5oGiWtAQAJ
I'm not sure exactly what is causing it, but a reproducible example has been posted, so I w…