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Hi, since the new installation of R and RStudio, I have been unable to run any mixed-model analysis in LinDA. I have tried natively in R and with RStudio with the same result. As long as it's a linear…
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**What is the method?**
Milo: differential abundance testing on KNN graphs https://www.biorxiv.org/content/10.1101/2020.11.23.393769v1
**Where is the code located?**
https://github.com/MarioniLab…
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**What is the method?**
DAseq https://www.biorxiv.org/content/10.1101/711929v3
**Where is the code located?**
https://github.com/KlugerLab/DAseq
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Thanks and regards as ever to the devs.
I'm considering several sets of 'omic data generated from the same cohort of ```FASTQ``` files (i.e. taxonomic, pathways, etc). The way of the CoDa seems a …
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Hi,
I am currently using MassLin2 to analyze my longitudinal microbiome dataset; however, I saw your recent paper describing LinDA and its strengths in comparison to MassLin2. Therefore, I would li…
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Hello Chi,
Thank you very much for your kind response by email. I attach the microtable (zip file) and the lines of code that you requested to solve my question.
[LEfSe.zip](https://github.com/C…
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## Friday, October 12
### Project Background
#### Prior Sample/Data Processing
* Samples collected from marine environments around the world
* Water sample collected
* Filtered to isolate vir…
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## Tasks
1. all PCGs BLAST all-vs-all search - diamond.py
2. gene sets construction
3. real alignments to respective sample contigs specific to gene coordinates
4. module detection of coverage-c…
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Hi,
I am having issue with a script "abundance_estimates_to_matrix.pl" with a view to generate cross sample normalized transcript matrix folllowing a tuitorial of Griffith lab (https://rnabio.org/mo…
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We're going to go [pytorch](https://www.pytorchlightning.ai/) OR [numpyro](https://github.com/pyro-ppl/numpyro). The framework will have the following skeleton
`model.py (mmvec.py)`
```python
…