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Dear Robert, Jeb and Francisco,
**Describe the issue**
I am working on a plant genome (~500Mb, het=1.29%). As the title mentioned, when I run RepeatModeler, LTR_retriever failed to generate a f…
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Hi, I am using the code provided in the tutorial and cannot to generate both heatmaps using the following code
```
heatmap.3(t(as.matrix(CNA.test[,4:ncol(CNA.test)])),dendrogram="r", distfun = fun…
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```
exp_mtx1
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Dear developers of sei,
First, thank you for developing this amazing tool.
I am doing variant effect prediction with sei and come up with this question.
Apart from the seqclass that is being aff…
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On some datasets THetA appears to exclude most intervals and fails as a result. Output:
=================================================
Arguments are:
Query Fil…
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Running ``sourmash plot --pdf --labels example.npy`` with ~200 signatures gives plots where the labels are too large and therefore overlap.
Looking at https://github.com/sourmash-bio/sourmash/blob/…
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I am trying to run PIQ for the 139 Jaspar motif on my dataset. However, I am getting an error during the clustering step.
The previous steps ran without a problem i.e. 'PWM hits across the genome' & …
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See also #28 (comparing clusters to Allen cell types)
- Nature Biotech paper (2018): [Dimensionality reduction for visualizing single-cell data using UMAP)](https://www.semanticscholar.org/paper/Di…
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I find that the "Number of blastp hits with different percentage identity" presented in p.5 of the output file Rplots.pdf could be a simple useful tool to estimate the blastp threshold to use to consi…
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Dear Prof. Barrick,
I regularly use breseq, finding it to be very powerful and valuable tool for my research.
I recently used gdtools PHYLOGENY to get the phylogenetic tree for my clonal samples…