TENxBUSData: TENxBUSData: 10x human and mouse cell mixture datasets in the...
In BUStools/TENxBUSData: Single cell dataset from 10x in BUS format

Description Usage Arguments Details Value Datasets Examples

View source: R/download.R

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.

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

`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.

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.

Character, directory to be used in BUSpaRse.