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Dear Yuqing,
Im working on a RNA-seq meta-analysis and trying to use ComBat-seq to normalize read counts previous to DESeq2 analysis. Im using the following command to normalize the counts within t…
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## Problem Statement
Data managers should have the ability to update and delete records from Metamist. Currently, there is limited ability to update records, and where there is, it's mostly confined …
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In the Experimental Assay we do not have an option for any type of computational analysis. A computational/bioinformatics analysis is also an experiment and I think we need to have an option for it.
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Hi! I have a question. I don't completely understand how the function filter_se() works. Specifically, this argument 'thr' despite the explanation shown in the source code: The dataset is filtered for…
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Hello,
Thank you very much for your package.
I have questions about model and K value settings in zinbwave function when combining with DESeq2.
I’m working on SMART-seqHT dataset of a specif…
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Proposal: allow more dry-lab assay classes (not all of them fit into ''Modelling analysis'')
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[//]: # (You can add comment regarding your issue hereafter)
### Comments
- tiny change to definition
- link with topics = epigenetics, epigenomics
[//]: # (End of issue comments)
### Hereafte…
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We only require `specimenID` for assay metadata files due to the heterogeneity of assay types provided.
There are cases where beginning an analysis can be blocked by missing metadata types, especi…
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Hi,
I have loaded the example dataset `'Hagai2018_mouse-lps'` from your Zenodo repository.
I am attempting to run DE genes analysis on the sctransformed data.
Your function `run_de` fails with er…
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This is a quick fix but users should know that when doing any kind of multiome analysis, `addGeneExpressionMatrix()` is not accurately calculating `Gex_MitoRatio`. There are two sources of error here …