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Gibbsdavidl / Immune-Subtype-Clustering

This repo contains the code necessary to reproduce the clusters found in "The Immune Landscape of Cancer".
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Some difficulties in running "app.R" #5

Open zhongjiehui opened 4 years ago

zhongjiehui commented 4 years ago

When I run "app.R" in the R 3.6.2 version, the program reported "Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install". How to solve this problem? Meanwhile, the program also reported "Error: argument "combatflag" is missing, with no default".Thank you!

huangwb8 commented 4 years ago

Hi！ I think the scripts in this project would not be updated and concerned by the authors any more, because their team had developed a new R package called "ImmuneSubtypeClassfier" in Github. After some tests long long ago, "ImmuneSubtypeClassfier" package worked! So you can visit here for more information

Gibbsdavidl commented 4 years ago

Thank you haungwb8. That's right. I would say if you want to see how the signature scores were computed, then the notebook concerned with that might be useful. But if you want to call immune subtypes, please use the ImmuneSubtypeClassifier. Thanks!

Gibbsdavidl commented 4 years ago

Hi @zhongjiehui

Please have a look at https://www.cri-iatlas.org/ for a working shiny app with the new tool built in.

This version of the subtype caller performs very badly, in general.

Thanks! -dave