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Hello,
I am trying to use SCnorm to normalize bulk RNA-seq data. I have about 10 studies with differing numbers of samples. I removed any genes that have no counts in any samples. I then used the a…
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https://github.com/LieberInstitute/Human_DLPFC_Deconvolution/tree/main
Add datasets to package:
- [x] Bulk RNA-seq
- [x] RNAScope proportions
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Sub-task of #2
- [ ] 1a. BrainSpan DLPFC bulk RNA-seq
- [ ] 1b. LIBD BrainSeq DLPFC data
- [ ] 1c. non-human primate laser microdissection (gene expression microarrays)
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The MC2 Center data model does not currently enable assay-specific metadata to be recorded. Adding these models is a critical part of supporting data sharing and reuse. Potential models to add were or…
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Related to a bullet point from [this comment](https://github.com/AlexsLemonade/training-modules/issues/240#issue-647525460) on the potential bulk RNA-seq changes inspired by 2020 May and 2020 June tra…
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[ ] Add a slide on publicly available data, how to access it and how to clean it up (maybe share a script for clean up?)
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Hello, very useful tool!
I learned the SenCID following the demo/SenCID_tutorial.ipynb. When I ran it more than one times, I can't get the consistant AUC values.
I seted adata.obs['condition'] as th…
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I am having an issue using Scissor to annotate bulk RNA sequencing (of paired tumor & normal samples) with single-cell tumor sequencing.
Here is my code:
```
## import bulk RNA seq data
bulk…
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Dear Tinyi Chu:
Hello!
My input of the Bulk RNA-seq is the combination of 3 batches, so I perform the cambat from SVM R packages to romve the batch effect. However, despite the original data are…
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Top-level issue to contain sub-tasks:
- [ ] in vivo cortex development bulk RNA-seq (#8)
- [ ] in vivo cortex development single-cell RNA-seq (#9)
- [ ] stem cell models of human cortex developm…