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Dear developers,
I have paired-end sequencing fastqc files from different samples and I would like to perform the phylogenetic abundance table based on the GTDB reference. Your singlem pipe tool ha…
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Thanks for developing Strainy!
I'm trying to use amplicon-based Nanopore reads to figure out strain abundances in bacterial samples. The pool has 740 strains and each sample may contain ~10 of them. …
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Hi. Great package!
Had a question regarding performing intra-sample abundance comparisons. Do you think this is feasible/appropriate to use scCODA for?
I.e. You have a covariate that doesn't de…
n-hal updated
4 months ago
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Dear developers,
First of all, thank you for creating this tool :)
I used mOTUs-extender to add 106 genomes to mOTU v3.0.1. Database creation went smoothly without errors or warning messages. …
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Hi,
When computing abundances i see a strange behaviour (see exemple below)
Each file processed individually and then grouped.
I would expect the sum of the two files should be 11+7=18 genes and …
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Hi there
We are having trouble using the newer versions of Kallisto, mainly all versions >=0.50.0 with the new index. Here is what I'm doing:
```bash
$ ./kallisto_0.50.1.sif kallisto index -i t…
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`agglomerateByRank` has `na.rm` parameter, but `agglomerateByVariable` does not. Is there a reason for this?
```R
library(mia)
data("GlobalPatterns", package = "mia")
tse
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```
I tried to get some graphs of warbler and sandpiper abundances for the months
where tropical events hit PR. There isn't enough coverage for 2004, and very
little for 2007. Is 2011 included in ou…
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Zou & Rudolf 2024 say: Priority effects: scenarios where the outcomes of species interaction depend on their relative arrival times or initial abundances.
But I wanted to compare to McPeek book def…
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[Solar abundances](https://github.com/andycasey/oracle/blob/master/si/code/elemdata.inc) are allegedly from before I was born. Needs updating.