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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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could not find function "AUCell_createViewerApp" #448

Open Eunice0519 opened 3 months ago

Eunice0519 commented 3 months ago

Hi,

I was trying to run this code and encountered an error: aucellApp <- plotTsne_AUCellApp(scenicOptions, exprMat_log) Error in AUCell_createViewerApp(auc = regulonAUC, thresholds = thresholds, : could not find function "AUCell_createViewerApp"

Appreciate if any one can provide more information on this issue. Thanks!

This is my session info.

R version 4.3.2 (2023-10-31) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.1.2

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Asia/Taipei tzcode source: internal

attached base packages: [1] grid parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] ggrepel_0.9.5 rhandsontable_0.3.8 rhdf5_2.46.1 Rcpp_1.0.12
[5] Matrix_1.6-5 stringr_1.5.1 plyr_1.8.9 magrittr_2.0.3
[9] ggplot2_3.4.4 gtable_0.3.4 gtools_3.9.5 gridExtra_2.3
[13] ArchR_1.0.2 shiny_1.8.0 doMC_1.3.8 iterators_1.0.14
[17] RColorBrewer_1.1-3 bigmemory_4.6.4 data.table_1.15.2 AUCell_1.25.2
[21] BiocParallel_1.36.0 doRNG_1.8.6 rngtools_1.5.2 foreach_1.5.2
[25] GENIE3_1.17.1 RcisTarget_1.23.1 SCENIC_1.3.1 SCopeLoomR_0.13.0
[29] SingleCellExperiment_1.22.0 SummarizedExperiment_1.32.0 Biobase_2.62.0 GenomicRanges_1.54.1
[33] GenomeInfoDb_1.38.6 IRanges_2.36.0 S4Vectors_0.40.2 BiocGenerics_0.48.1
[37] MatrixGenerics_1.15.0 matrixStats_1.2.0

or-lazarescu commented 3 months ago

i encountered the same issue. tried to solve it by sourcing the code for "AUCell_createViewerApp" from AUCell source code (downloaded the folder from: https://bioconductor.org/packages/release/bioc/html/AUCell.html). it still doesn't work because rbokeh was removed from bioconductor (from AUCell commit history)

ghuls commented 2 months ago

rbokeh was removed from BioConductor and AUCell was not allowed to depend on it anymore, so the plotTsne_AUCellApp viewer was removed too: https://github.com/aertslab/AUCell/issues/42