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The TCGA firehose data download on [tcga.Rmd line 49](https://github.com/genomicsclass/labs/blob/9ac47c7099a8a2452813c4bb675c21010f5becec/biocadv_6x/tcga.Rmd#L49) throws an error stating the connectio…
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Hi there,
I seem to be having some issues running XGR's liftover function, which now returns some errors related to "Chain". Is there something else I need to install?
## Example
```R
## Cons…
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I'm just using 3 input fastq files with 10k reads each, as just a test.
My workflow:
```r
config_file = FLAMES::create_config(outdir, type = "sc_3end", do_barcode_demultiplex = TRUE)
sce = …
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Observed the following error when using `plotRegion()` on a grouped counts object (9 groups). Also observed in other datasets when plotting larger numbers of groups (MP).
Call:
`options(repr…
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Hello,
I'm trying to query subsets of Roadmap bed.gz files. However there seems to be some issues here:
## Reprex
### Code
```R
URL
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Hi
When I run sleuth_live(so), the tab for "scatter plots" gives this error (only for the first plot):
Error in as.data.frame.default: cannot coerce class "c("quosure", "formula")" to a data.fr…
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Hello,
`rtracklayer` has been great for importing various supplementary files from GEO. However, I've run into the following error when trying to import certain bigWig files.
A couple of notes…
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## 1. Bug description
PolyFun is not installed. Reinstall echofinemap with PolyFun? This will automatically restart R. (y/n):
Error in echofinemap::POLYFUN_install() : PolyFun is not installed.
…
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## 1. Bug description
`finemap_loci()` errors out with `conditioned_snps must have a length equal to 1 or the number of loci`
## 2. Reproducible example
### Code
```R
columnnames
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Hello Yuichi. I've been trying out `pmsignature`. Thanks for the package!
I just wanted to report an apparent bug that prevents the visualization of the Kth (last) mutation signature. After following…