GenomeInfoDb

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Caching seqinfo

7

Hi, my package uses genomeInfoDb, and we use the seqlevelsStyle function to clean up user-inputted data and ensure consistent chromosome names (in our case, we go with NCBI style, which...

jeff-mandell

error: seqlevelsStyle(annotations) <- 'UCSC'

8

Hi, I got error message: > annotations seqlevelsStyle(annotations)

Kateahn

Error on setting `seqlevelsStyle(gal) <- "RefSeq"`

4

hi, setting `seqlevelsStyle()` to `RefSeq` works for, e.g., `TxDb` objects, but it gives an error with `GenomicAlignment` objects. Here is a minimal repex: ```r library(GenomicAlignments) library(TxDb.Hsapiens.UCSC.hg38.knownGene) txdb

rcastelo

seqlevelsStyle -- supporting offline use?

1

when setting seqlevelsStyle to "UCSC" it appears a network query is inevitably issued, leading to failure if off line. can we use BiocFileCache to hold the relevant information persistently? would...

vjcitn

Mapping Ensembl seqlevels to UCSC for Mmul_10/rheMac10

2

> Hi Hervé, > > Happy New Year! > > I’m working with Macaque single cell ATAC-seq data recently, and the package Signac requires the annotation formatted to UCSC style....

hpages

Provide a complete mapping of UCSC chromosome names to Ensembl

1

@ivanek opened an issue over at `ensembldb` (https://github.com/jotsetung/ensembldb/issues/88). `ensembldb` in general uses the `genomeStyles` function from `GenomeInfoDb` to map chromosome names. As of now we can *only* map the standard...

jorainer

Mitocondrial chromosome naming, seqlevelsStyle()

4

I thanks for a nice function, I use seqlevelsStyle a lot. One thing has always bothered me, is for the mitocondrial chromosome. Two objects with same naming convention as these:...

Roleren