In BUStools/TENxBUSData: Single cell dataset from 10x in BUS format

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

This package provides the barcode, UMI, and set (BUS) format of the following datasets from 10X genomics:

• 100 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells (v2 chemistry)
• 1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells (v3 chemistry)
• 1k PBMCs from a Healthy Donor (v3 chemistry)
• 10k Brain Cells from an E18 Mouse (v3 chemistry)

The original fastq files have already been processed into the BUS format, which is a table with the following columns: barcode, UMI, equivalence class/set, and count (i.e. number of reads for the same barcode, UMI, and set). The datasets have been uploaded to ExperimentHub. This vignette demonstrates how to download the first dataset above with this package. See the BUSpaRse website for more detailed vignettes.

library(TENxBUSData)
library(ExperimentHub)

See which datasets are available with this package.

eh <- ExperimentHub()
listResources(eh, "TENxBUSData")

In this vignette, we download the 100 cell dataset. The force argument will force redownload even if the files are already present.

TENxBUSData(".", dataset = "hgmm100", force = TRUE)

Which files are downloaded?

list.files("./out_hgmm100")

These should be sufficient to construct a sparse matrix with package BUSpaRse.

BUStools/TENxBUSData documentation built on May 8, 2020, 4:20 a.m.