An R package for basic indrop analyses and data handling
devtools::install_github("caleblareau/indRop")
Not a lot presently. What you can do as of version 0.1.0:
readIndrop
imports the data to a sparse matrix format that can be quickly incorporated into a Seurat objectexport10X
to write a sparse matrix that was imported into the 3 file format that's typical of 10X data. Here's a basic emaple of importing multiple indrops datasets and then using them to create a Seurat object.
library(Seurat)
data1 <- "S1.counts.tsv"
data2 <- "S2.counts.tsv"
sm <- readIndrop(c(data1,data2))
seuratObject <- new("seurat", raw.data = sm)
Here's a basic emaple of importing multiple indrops datasets and then exporting them to a
folder such that the files resemble what 10X usually spits out of CellRanger. Here, these
three files will be sent to the variable defined by outFolder
.
data1 <- "S1.counts.tsv"
data2 <- "S2.counts.tsv"
outFolder <- "output1"
sm <- readIndrop(c(data1,data2))
export10X(sm, outFolder)
This package is designed to plug a gap between the indrops pipeline and Seurat.
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