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Hello,
Can we used velocyto to analysis bulk RNA seq data. We want used this wonderful methods to do the same analysis juts like the smart-seq2 pipeline you have showed us, because we just want to…
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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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Thank you for developing this useful package. I wonder how we can retrain SenCID with a new set of bulk RNA-seq data for training? Would it be possible to provide the source code for training the SenC…
zji90 updated
5 months ago
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Hi,
I have a mouse bulk RNA seq data, can I use xcell to do immune cell infiltration analysis?
Best,
Honglin
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Hello!
I have a new problem: The get_xy_label_data_cnn_combine_from_database.py report an error when generate NEPDF data for the example sc-RNA seq h5 file
`python CNNC/get_xy_label_data_cnn_combine…
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I am trying to use GSE124872 to annotate bulk RNA seq data but I'm having trouble creating an expression set from both of them. For GSE124872, there is no actually cell type in the metadata that is co…
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Hi,
I am trying to get the celldex::MousebulkRNA-seq() and get the following error. I've tried to run on both mac and windows with the same error. Any advice on how to rectify appreciated.
Error: fa…
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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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Hello,
I was wondering if it is more appropriate to use the v1 standard kallisto index https://github.com/pachterlab/kallisto-transcriptome-indices/releases for bulk RNA seq data compared to an ind…
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For some reason, a very large portion of the values in the `p`, `padj`, and `lfc` arrays are NAs and I'm not sure why. I am using the raw counts for the bulk RNA-seq as input to CAR-seq.
Any help …