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Comment: unable to install.packages("spatialLIBD")
by
Leonardo Collado Torres
▴
1000
All the solutions Lori proposed are valid. The `STexampleData` package I think has only 1 of our samples (see https://bioconductor.org/pack…
Answer: how to use Rsamtools to parse extra fields from STAR alignment
by
Martin Morgan
25k
The 'extra columns' are called 'tags' in the SAM specification. Following the documentation `?ScanBamParam` you should add `tag = "NH"`. Se…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip
by
Delta._.43
▴
10
Yes, indeed it is the same error. Here are the first few lines of my count file.
```
"ENSG00000000003":"001" 0
"ENSG00000000003":"002" 1032…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip
by
Alejandro Reyes
★
1.8k
Thanks for your detail post. I think this might be related to this issue here: https://support.bioconductor.org/p/9143537/
Just to verify…
Answer: spot- vs cell-level data access
by
Leonardo Collado Torres
▴
1000
Hi,
The `SingleCellExperiment` object you can download with `fetch_data(type = "sce")` pre-dates the creation of `SpatialExperiment`. No…
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