Package 'TabulaMurisSenisData'

Title: Bulk and single-cell RNA-seq data from the Tabula Muris Senis project
Description: This package provides access to RNA-seq data generated by the Tabula Muris Senis project via the Bioconductor project. The data is made available without restrictions by the Chan Zuckerberg Biohub. It is provided here without further processing, collected in the form of SingleCellExperiment objects.
Authors: Charlotte Soneson [aut, cre] (ORCID: <https://orcid.org/0000-0003-3833-2169>), Dania Machlab [aut] (ORCID: <https://orcid.org/0000-0002-2578-6930>), Federico Marini [aut] (ORCID: <https://orcid.org/0000-0003-3252-7758>), Stefania Astrologo [aut] (ORCID: <https://orcid.org/0000-0002-4845-2802>)
Maintainer: Charlotte Soneson <[email protected]>
License: MIT + file LICENSE
Version: 1.18.0
Built: 2026-10-10 11:16:36 UTC
Source: https://github.com/bioc/TabulaMurisSenisData

Help Index

List available tissues for the Tabula Muris Senis datasets

Description

List available tissues for the Tabula Muris Senis datasets

Usage

listTabulaMurisSenisTissues(dataset)

Arguments

dataset

Either 'Droplet' or 'FACS'

Value

A character vector with the available tissues for the indicated dataset.

Examples

listTabulaMurisSenisTissues(dataset = "Droplet")

Access the Tabula Muris Senis bulk RNA-seq data

Description

Access the bulk RNA-seq data from the Tabula Muris Senis consortium.

Usage

TabulaMurisSenisBulk(infoOnly = FALSE)

Arguments

infoOnly

Logical scalar. If TRUE, only print the total size of the files that will be downloaded to and/or retrieved from the cache.

Details

The data set was downloaded from GEO (accession number GSE132040). The summary statistics from HTSeq-count were combined with the provided sample metadata and included in the colData of the object. In addition, gene annotations from GENCODE vM19 were downloaded and included in the rowRanges of the object.

Value

If infoOnly is FALSE, return a SingleCellExperiment object with a single matrix of counts. Otherwise, return 'NULL'.

Author(s)

Charlotte Soneson

References

Schaum et al (2019): The murine transcriptome reveals global aging nodes with organ-specific phase and amplitude. bioRxiv doi:10.1101/662254.

The Tabula Muris Consortium (2020): A single-cell transcriptomic atlas characterizes ageing tissues in the mouse. Nature 583:590–595.

Examples

if (interactive()) {
  sce <- TabulaMurisSenisBulk()
}

Access the Tabula Muris Senis droplet single-cell RNA-seq data

Description

Access the droplet (10x Genomics) RNA-seq data from the Tabula Muris Senis consortium.

Usage

TabulaMurisSenisDroplet(
  tissues = "All",
  processedCounts = FALSE,
  reducedDims = TRUE,
  infoOnly = FALSE
)

Arguments

tissues

A character vector with the tissues to retrieve objects for. A list of available tissues can be obtained using listTabulaMurisSenisTissues("Droplet").
processedCounts

Logical scalar. If TRUE, include the processed counts in addition to the raw counts in the SingleCellExperiment object.
reducedDims

Logical scalar. If TRUE, include the PCA, tSNE and UMAP representations in the SingleCellExperiment object (the tSNE representation is not available for the full dataset ('All' tissue)).
infoOnly

Logical scalar. If TRUE, only print the total size of the files that will be downloaded to and/or retrieved from the cache.

Details

The data set was downloaded from figshare (https://figshare.com/articles/dataset/Processed_files_to_use_with_scanpy_/8273102?file=23938934 for the full data set, https://figshare.com/articles/dataset/Tabula_Muris_Senis_Data_Objects/12654728 for the individual tissue ones).

Value

If infoOnly is FALSE, returns a named list of SingleCellExperiment objects (one per tissue requested via tissues). Otherwise, each element in the list is 'NULL'.

Author(s)

Charlotte Soneson

References

Schaum et al (2019): The murine transcriptome reveals global aging nodes with organ-specific phase and amplitude. bioRxiv doi:10.1101/662254.

The Tabula Muris Consortium (2020): A single-cell transcriptomic atlas characterizes ageing tissues in the mouse. Nature 583:590–595.

Examples

if (interactive()) {
  sce <- TabulaMurisSenisDroplet(tissues = "All")
}

Get the Tabula Muris Senis FACS single-cell RNA-seq data

Description

Access the FACS (Smart-Seq2) RNA-seq data from the Tabula Muris Senis consortium.

Usage

TabulaMurisSenisFACS(
  tissues = "All",
  processedCounts = FALSE,
  reducedDims = TRUE,
  infoOnly = FALSE
)

Arguments

tissues

A character vector with the tissues to retrieve objects for. A list of available tissues can be obtained using listTabulaMurisSenisTissues("FACS").
processedCounts

Logical scalar. If TRUE, include the processed counts in addition to the raw counts in the SingleCellExperiment object.
reducedDims

Logical scalar. If TRUE, include the PCA, tSNE and UMAP representations in the SingleCellExperiment object (the tSNE representation is not available for the full dataset ('All' tissue)).
infoOnly

Logical scalar. If TRUE, only print the total size of the files that will be downloaded to and/or retrieved from the cache.

Details

The data set was downloaded from figshare (https://figshare.com/articles/dataset/Processed_files_to_use_with_scanpy_/8273102?file=23937842 for the full data set, https://figshare.com/articles/dataset/Tabula_Muris_Senis_Data_Objects/12654728 for the individual tissue ones).

Value

If infoOnly is FALSE, returns a named list of SingleCellExperiment objects (one per tissue requested via tissues). Otherwise, each element in the list is 'NULL'.

Author(s)

Charlotte Soneson

References

Schaum et al (2019): The murine transcriptome reveals global aging nodes with organ-specific phase and amplitude. bioRxiv doi:10.1101/662254.

The Tabula Muris Consortium (2020): A single-cell transcriptomic atlas characterizes ageing tissues in the mouse. Nature 583:590–595.

Examples

if (interactive()) {
  sce <- TabulaMurisSenisFACS(tissues = "All")
}