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Hi Tinyi,
Quick question. Are the inferred cell-type specific expression matrices normalized for varying library size of samples/spots? In the vignette for downstream analysis you suggest performin…
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Hello, i have big interests of your Mesomics project, so i just try to do similar analyses with other cancer datasets.
However i keep struggling to do mapping the feature to ternary plot like below. …
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To assess the affects of tumor purity on our results, we should re-run certain survival models, considering only samples that have `tumor_fraction>= median tumor fraction` (https://github.com/AlexsLem…
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Dear sciCNV developers,
I have 2 questions about sciCNV regarding control cell selection and multiple baseline feature.
Firstly, I would like to ask if gene expression data from control cells of…
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Hi! I would like to change the group color in plot_dimred, but it doesn't work. Can you help me? Here is my code:
**plot_dimred(
model, alpha_cells=0.4,color_cells = "grouping",
expression_so…
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Thank you very much for your work, and I would like to ask you how to reproduce the images of the tumor results you analyzed in the article and How to get Hub gene of co-expression module ?
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Hey Guys,
I came across what may/may not be a bug in Topiary that specifically pertains to the use of NetMHC, but not other callers that then call NetMHC (NetMHCcons). I ran:
```
jpf-mbp:test johnfi…
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I found an article called"Attention Gate ResU-Net for automatic MRI brain tumor segmentation"in IEEE,and I want to know if it is the corresponding article.I leave the abstract below,and I will be appr…
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```
URL of the application, including the query parameters that specify the
filter:http://explorer.cancerregulome.org/all_pairs/?dataset=kirc_01oct12_A_pw&t
_label=aldh4a1
Using KIRC data set with tu…
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Hi!
I really like your tool! I need to calculate differential expression between certain spots like you did in Figure 6c / 6d of your paper "Estimation of cell lineages in tumors from spatial trans…