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Step 2 Not Working #21

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sgrudz opened this issue Apr 20, 2023 · 1 comment
Open

Step 2 Not Working #21

sgrudz opened this issue Apr 20, 2023 · 1 comment

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@sgrudz
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sgrudz commented Apr 20, 2023

STEP2: Load annotation databases: Ularcirc comes with one existing data set that has been aligned to hg38. While annotation is not required to identify circRNAs we recomment to download the respective human annotation databases as follows:

if (!requireNamespace("BiocManager", quietly=TRUE))
        install.packages("BiocManager")

\dontrun { 
  BiocManager::install(c("BSgenome.Hsapiens.UCSC.hg19",         # Genome; enables sequence analysis
                      "TxDb.Hsapiens.UCSC.hg19.knownGene",    # Transcript database
                      "org.Hs.eg.db"))                        # Annotation database
      }

When I run this, it says Error: unexpected symbol in "\dontrun"

@davhum
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davhum commented Dec 13, 2023

Run just the following command

BiocManager::install(c("BSgenome.Hsapiens.UCSC.hg19", # Genome; enables sequence analysis
"TxDb.Hsapiens.UCSC.hg19.knownGene", # Transcript database
"org.Hs.eg.db"))

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