Processing and working with indrops data

An R package for basic indrop analyses and data handling

Install

devtools::install_github("caleblareau/indRop")

Functionality

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 object
• export10X to write a sparse matrix that was imported into the 3 file format that's typical of 10X data.

Import

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)

Export

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)

Description

This package is designed to plug a gap between the indrops pipeline and Seurat.