In shooshtarilab/TMExplorer: A Collection of Tumour Microenvironment Single-cell RNA Sequencing Datasets and Corresponding Metadata

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

library(TMExplorer)

Introduction

TMExplorer (Tumour Microenvironment Explorer) is a curated collection of scRNAseq datasets sequenced from tumours. It aims to provide a single point of entry for users looking to study the tumour microenvironment at the single-cell level.

Users can quickly search available datasets using the metadata table, and then download the datasets they are interested in for analysis. Optionally, users can save the datasets for use in applications other than R.

This package will improve the ease of studying the tumour microenvironment with single-cell sequencing. Developers may use this package to obtain data for validation of new algorithms and researchers interested in the tumour microenvironment may use it to study specific cancers more closely.

Exploring available datasets

Start by exploring the available datasets through metadata.

res = queryTME(metadata_only = TRUE)

knitr::kable(head(res[[1]][,1:5]))

This will return a list containing a single dataframe of metadata for all available datasets. View the metadata with View(res[[1]]) and then check ?queryTME for a description of searchable fields.

Note: in order to keep the function's interface consistent, queryTME always returns a list of objects, even if there is only one object. You may prefer running res = queryTME(metadata_only = TRUE)[[1]] in order to save the dataframe directly.

The metatadata_only argument can be applied alongside any other argument in order to examine only datasets that have certain qualities. You can, for instance, view only breast cancer datasets by using

res = queryTME(tumour_type = 'Breast cancer', metadata_only = TRUE)[[1]]

knitr::kable(head(res[,1:5]))

Search Parameter | Description | Examples
---------------- | ----------------------------------------------- | ----------------------- geo_accession | Search by GEO accession number | GSE72056, GSE57872
score_type | Search by type of score shown in $expression | TPM, RPKM, FPKM
has_signatures | Filter by presence of cell-type gene signatures | TRUE, FALSE
has_truth | Filter by presence of cell-type labels | TRUE, FALSE
tumour_type | Search by tumour type | Breast cancer, Melanoma author | Search by first author | Patel, Tirosh, Chung
journal | Search by publication journal | Science, Nature, Cell
year | Search by year of publication | <2015, >2015, 2013-2015 pmid | Search by publication ID | 24925914, 27124452
sequence_tech | Search by sequencing technology | SMART-seq, Fluidigm C1
organism | Search by source organism | Human, Mice
sparse | Return expression in sparse matrices | TRUE, FALSE

: (#tab:table1) Search parameters for queryTME alongside example values.

Searching by year

In order to search by single years and a range of years, the package looks for specific patterns. '2013-2015' will search for datasets published between 2013 and 2015, inclusive. '<2015' or '2015>' will search for datasets published before or in 2015. '>2015' or '2015<' will search for datasets published in or after 2015.

Getting datasets

Once you've found a field to search on, you can get your data. For this example, we're pulling a specific dataset by its GEO ID.

res = queryTME(geo_accession = "GSE81861")

This will return a list containing dataset GSE72056. The dataset is stored as a SingleCellExperiment object, which has the following metadata list

| Attribute | Description | | ------------- | --------------------------------------------------------------- | | signatures | A data.frame containing the cell types and a list of genes that represent that cell type | | cells | A list of cells included in the study | | genes | A list of genes included in the study | | pmid | The PubMed ID of the study | | technology | The sequencing technology used | | score_type | The type of score shown in tme_data$expression | | organism | The type of organism from which cells were sequenced | | author | The first author of the paper presenting the data | | tumour_type | The type of tumour sequenced | | patients | The number of patients included in the study | | tumours | The number of tumours sampled by the study | | geo_accession | The GEO accession ID for the dataset |

: (#tab:table2) Metadata attributes in the SingleCellExperiment object.

To access the expression data for a result, use

View(counts(res[[1]]))

knitr::kable(head(counts(res[[1]])[,1:2]))

Cell type labels are stored under colData(res[[1]]) for datasets for which cell type labels are available

Metadata is stored in a named list accessible by metadata(res[[1]]). Specific entries can be accessed by attribute name.

metadata(res[[1]])$pmid

Example: Returning all datasets with cell-type labels

Say you want to measure the performance of cell-type classification methods. To do this, you need datasets that have the true cell-types available.

res = queryTME(has_truth = TRUE)

This will return a list of all datasets that have true cell-types available. You can see the cell types for the first dataset using the following command:

View(colData(res[[1]]))

knitr::kable(head(colData(res[[1]])))

The first column of this dataframe contains the cell barcode, and the second contains the cell type.

Example: Returning all datasets with cell-type labels and cell-type gene signatures

Some cell-type classification methods require a list of gene signatures, to return only datasets that have cell-type gene signatures available, use:

res = queryTME(has_truth = TRUE, has_signatures = TRUE)
View(metadata(res[[1]])$signatures)

knitr::kable(metadata(res[[1]])$signatures[,1:3])

Saving Data

To facilitate the use of any or all datasets outside of R, you can use saveTME(). saveTME takes two parameters, one a tme_data object to be saved, and the other the directory you would like data to be saved in. Note that the output directory should not already exist.

To save the data from the earlier example to disk, use the following commands.

res = queryTME(geo_accession = "GSE72056")[[1]]
saveTME(res, '~/Downloads/GSE72056')

The result is three CSV files that can be used in other programs. In the future we will support saving in other formats.

Session Information

sessionInfo()

shooshtarilab/TMExplorer documentation built on June 7, 2022, 1:31 p.m.