Package 'TENxBUSData'

TENxBUSData: 10x human and mouse cell mixture datasets in the BUS format

Description

This package provides 5 10x datasets in the BUS format, to be downloaded from within R. The files downloaded from this package are sufficient to generate a sparse matrix with package BUSpaRse to be used for downstream analysis with Seurat. Human and mouse transcriptomes from Ensembl version 99 were used to generate the BUS format from FASTQ files. This package server the following purposes: First, to demonstrate the kallisto bus workflow and downstream analyses. Second, for advanced users to experiment with other ways to collapse UMIs mapped to multiple genes and with other ways of barcode correction. The datasets are on ExperimentHub.

This function will download the 10x datasets, already processed and stored in the BUS format, from ExperimentHub. This function will decompress the downloaded file and return the directory where the files necessary to construct the sparse matrix with BUSpaRse are located.

Usage

TENxBUSData(
  file_path,
  dataset = c("hgmm100", "hgmm1k", "pbmc1k", "neuron10k"),
  force = FALSE,
  verbose = TRUE
)

Arguments

file_path	Character vector of length 1, specifying where to download the data.
dataset	Character, must be one of "hgmm100", "hgmm1k", "pbmc1k", "neuron10k".
force	Logical, whether to force redownload if the files are already present. Defaults to FALSE.
verbose	Whether to display progress of download.

Details

The following files will be downloaded:

matrix.ec

Text file with 2 columns. The first column is the index of equivalence classes used in BUS files. The second column is the equivalence classes themselves, consisted of sets of transcript indices from the kallisto index.

output.sorted

Binary BUS file sorted by barcode, UMI, and equivalence classes. This can be directly parsedd by bustools to get the gene count matrix.

output.sorted.txt

Sorted BUS file in text form. This is to be used with BUSpaRse to get the gene count matrix.

transcripts.txt

Transcripts included in the BUS data, in the same order as in the kallisto index.

The gzipped file downloaded from ExperimentHub will be in a cache directory that can be retrieved by getExperimentHubOption("CACHE"). The cache will remain even if the decompressed files in the directory specified when calling this function are deleted. To delete cache, use removeCache.

Value

Character, directory to be used in BUSpaRse.

Datasets

hgmm100

100 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells. The raw data can be found here: https://support.10xgenomics.com/single-cell-gene-expression/datasets/2.1.0/hgmm_100

hgmm1k

1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells (v3 chemistry). The raw data can be found here: https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0/hgmm_1k_v3

pbmc1k

1k PBMCs from a Healthy Donor (v3 chemistry). The raw data can be found here: https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0/pbmc_1k_v3

neuron10k

10k Brain Cells from an E18 Mouse (v3 chemistry). The raw data can be found here: https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0/neuron_10k_v3

Examples

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

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