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The dataset posted on Zenodo only contains the immune cells. Are the tumor cells available somewhere?
I checked the "Integration" directory where it says the input datasets (individual projects) ar…
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I am able to successfully run the GRN step, but the CTX step never finishes executing. The last line of the log says "Writing to file," and a file is created with appropriate rows and columns, but the…
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https://mp.weixin.qq.com/s/lHG1F5Pmkixfkxi80M8D2w
ixxmu updated
2 years ago
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Hello,
Infercnv is failing on step 15:
STEP 15: computing tumor subclusters via leiden
INFO [2022-03-21 12:10:37] define_signif_tumor_subclusters(p_val=0.1
INFO [2022-03-21 12:10:37] define_…
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In the results line 204, we write:
> In addition, the tumor purity of these two LFS samples was low (16% and 37%, respectively), suggesting the classifier may require a certain level of tumor purity…
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https://mp.weixin.qq.com/s/k6iQgkL67BYmQBPdWBCPIA
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#### Major use case: tumor-immune.
Immune/PanCK- cells are defined a priori via ioprofiles, and tumor/epithelial PanCK+ cell are not.
#### An approach that should work:
- Split cells into PanCK…
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https://mp.weixin.qq.com/s/_Z5mWDNi8hzAc_mLivcjsQ
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Hello inferCNVpy,
It seems `vmin` and `vmax` don't work for `cnv.pl.chromosome_heatmap()`. Appreciate it if you could tell us How to adjust the scale bar of chromosome_heatmap.
Thanks!
Best,
YJ
…
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Without looking too deeply through the code, is there anything specifically inhibiting the use of bulk RNA-seq with inferCNV (e.g. thinking regarding any model assumptions being implemented)? Thanks f…