Workflow Steps and Code Snippets

1 tagged steps and code snippets that match keyword EnsDb.Mmusculus.v79

Code to reproduce analyses shown in the Signac paper 

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library(Signac)
library(EnsDb.Mmusculus.v79)
library(EnsDb.Hsapiens.v75)
library(GenomeInfoDb)

# extract gene annotations from EnsDb
annotations.mm <- GetGRangesFromEnsDb(ensdb = EnsDb.Mmusculus.v79)
annotations.hg <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v75)

# change to UCSC style since the data was mapped to hg19/mm10
seqlevelsStyle(annotations.hg) <- 'UCSC'
genome(annotations.hg) <- "hg19"

seqlevelsStyle(annotations.mm) <- 'UCSC'
genome(annotations.mm) <- "mm10"

# save
saveRDS(object = annotations.mm, file = "data/biccn/annotations.rds")
saveRDS(object = annotations.hg, file = "data/pbmc_atac/annotations.rds")
R EnsDb.Hsapiens.v75 EnsDb.Mmusculus.v79 Signac GenomeInfoDb From line 1 of downsampling_code/get_annotations.R
data / bioconductor

EnsDb.Mmusculus.v79

Ensembl based annotation package: Exposes an annotation databases generated from Ensembl.

author: Johannes Rainer
library: r:EnsDb.Mmusculus.v79
license: Artistic-2.0
version: 2.99.0
biocViews: ['AnnotationData', 'EnsDb', 'Mus_musculus']
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