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**Problem**:
Polis currently sets k for k-means to 2-5 groups and chooses the best k using silhouette coefficient to determine opinion groups.
This was chosen for explainability and visualization b…
avivo updated
2 years ago
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Hi,
I need to generate radial trees similar to those presented in Jaspar Database including the TF hit ID directly in the tree. https://jaspar.genereg.net/matrix-clusters/urochordates/.
However, whe…
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Is there any way to extract the connectivity or consensus matrix for a multi-run nmf object that is based on the rows rather than the columns (samples)? I want to be able to extract the basis W matrix…
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Hi,
I have been interested in using your pipeline with ONT long-read data with UMIs that are generated by colleagues in my lab.
To begin with, I tried to execute the pipeline with the example data…
camcl updated
1 month ago
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Hello Kristoffer,
I ran `NGSpeciesID` with the following command:
```
for file in *.fastq; do
NGSpeciesID --t 4 --ont --fastq $file \
--consensus --medaka \
--abundance_ratio 0.005 \
--rc…
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Hi team,
I am using this as part of https://github.com/epi2me-labs/wf-transcriptomes/
I am able to run make batches, generating 0-48 batches, and the following clustering step failed.
The error …
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Hi
I am running isONclust in a Conda environment and the spoa and medaka modules are loaded before the run.
Here is my commands:
```
ml Miniconda3/4.10.3
source activate isonclust
ml spoa/…
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Hello,
could you please give an update on what you consider the best way to choose the best tree at the moment?
I see that we could try taking the one with the lowest nlgLH (normalized log likeli…
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A cool feature to add to the package would be a **consensus heatmap** to visualize the consensus matrix, and you could add a covariate bar for cluster assignments.
For example, something similar to…