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Hi,
I have come across the need to analyse GeoMx data that is generated in two different instances. I have successfully run your tool in two separate instances but as these two projects are related…
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@mandichen
Hi，mandichen
Good job and I am very interested in your research, but I have some questions.I used the sample data BM2_v0s0_n_200.h5ad and Macosko_cell_cycle_genes.txt to get the follow…
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Hi, mikelove, I used to apply DESeq2 to analysis bulk RNA-seq dataset, where we can correct for the batch effects by including them in the design matrix of DESeq2. further, by combining zinbwave with …
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I think, in this part, top_genes and bottom_genes have some overlap. If you set nlabel ==20, and print the data of top_genes and bottom_genes, you can find the overlap.
top_genes % arrange(padj) …
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To test CDSeq, I used counts from published bulk RNA-seq of human skin (accession numbers below). Gene-level counts were used as input. Surprisingly, estProp from the output always distributes the pro…
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I read through the paper and went through the tutorial and I am having trouble figuring out how to best use the outputs. From the outputs is it possible to get cell type specific counts for each gene …
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Would it be possible to implement a function that can plot (for a given gene set) a GSEA plot similar to the one here:
[https://yulab-smu.top/biomedical-knowledge-mining-book/enrichplot.html#runnin…
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Hi,
I am trying to use Clipper to do the **differential analysis** on my data, which is a single-cell dataset collected from **multiple subjects**. I found the example data included in the package …
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Hi,
I have bulk RNA-seq from islets cell populations (alpha, beta, delta cells etc.), and am interested in analyzing the content of each sample.
For example, I would like to know for a sample lab…
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Hi~
I also try to run tutorial 4 and I met a problem about step 1. I'm not setting 'CIBERSORTx fractions Singularity path' but it didn't run on default Docker, instead it shows that it wants to run …