In vjcitn/osca4anvil: Simplify production of computable OSCA texts and artifacts for AnVIL

Introduction

This package includes scripts that acquire and install selected versions of the OSCA book for single-cell genomics.

Approach using a default cloud environment in AnVIL

The following steps work with sources from Bioconductor 3.19.

BiocManager::install("vjcitn/osca4anvil", ref="bioc319")
library(osca4anvil)
clone_osca(branch="RELEASE_3_19")
lapply(osca4anvil::packs(), osca4anvil::get_deps, 
  installer=function(x) BiocManager::install(x, ask=FALSE))

Limited confirmation:

library(scRNAseq)
sce.416b <- LunSpikeInData(which="416b")
library(AnnotationHub)
ens.mm.v97 <- AnnotationHub()[["AH73905"]]
chr.loc <- mapIds(ens.mm.v97, keys=rownames(sce.416b),
keytype="GENEID", column="SEQNAME")
is.mito <- which(chr.loc=="MT")
library(scuttle)
df <- perCellQCMetrics(sce.416b, subsets=list(Mito=is.mito))
low.lib <- isOutlier(df$sum, type="lower", log=TRUE)
table(low.lib)

vjcitn/osca4anvil documentation built on May 22, 2024, 10:23 a.m.