:chart_with_upwards_trend:SeqPlots - An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps.
I was trying to use the getPlotSetArray() function, but I got the error 'No genomes installed!' from the getREF function. I digged into the problem and it turns out that in the latest version of the BSgenome package the output of the function BSgenome::installed.genomes(splitNameParts=TRUE) changed from:
_pkgname organism provider providerversion masked
1 BSgenome.Hsapiens.UCSC.hg38 Hsapiens UCSC hg38 FALSE
to
pkgname organism provider genome masked
1 BSgenome.Hsapiens.UCSC.hg38 Hsapiens UCSC hg38 FALSE
To fix the error I added at line 94 of the helper_functions.R script the new line:
if( !length(GENOMES) ) GENOMES <- BSgenome::installed.genomes(splitNameParts=TRUE)$genome
I was trying to use the getPlotSetArray() function, but I got the error 'No genomes installed!' from the getREF function. I digged into the problem and it turns out that in the latest version of the BSgenome package the output of the function BSgenome::installed.genomes(splitNameParts=TRUE) changed from: _pkgname organism provider providerversion masked 1 BSgenome.Hsapiens.UCSC.hg38 Hsapiens UCSC hg38 FALSE to pkgname organism provider genome masked 1 BSgenome.Hsapiens.UCSC.hg38 Hsapiens UCSC hg38 FALSE To fix the error I added at line 94 of the helper_functions.R script the new line: if( !length(GENOMES) ) GENOMES <- BSgenome::installed.genomes(splitNameParts=TRUE)$genome
Hope this helps!