The data from the
recount3 project is accessible through R/Bioconductor packages as well as raw files. You can access the data through:
- recount3: this R/Bioconductor package retrieves the data from the IDIES servers and builds
RangedSummarizedExperimentobjects by study that can be used with many Bioconductor analysis packages for downstream analyses (DOI: 10.1038/nmeth.3252).
- snapcount: this R/Bioconductor package also provides access to data from
recount3through a query-based interface.
- raw files: these are text files that are hosted by IDIES and can be used with other programming software outside of R.
As noted in the Bioconductor chapter, longer tutorials (called vignette documents in R/Bioconductor) showing how to install and use our R/Bioconductor packages are available from the Bioconductor landing pages (that is, the Bioconductor website for each package), such as the one called
recount3 quick start guide.
## Install the recount3 R/Bioconductor package if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") ::install("recount3") BiocManager ## Load recount3 R package library("recount3") ## Find all available human projects <- available_projects() human_projects ## Find the project you are interested in, ## here we use SRP009615 as an example <- subset( proj_info human_projects,== "SRP009615" & project_type == "data_sources" project ) ## Create a RangedSummarizedExperiment (RSE) object at the gene level <- create_rse(proj_info) rse_gene_SRP009615 ## Explore that RSE object rse_gene_SRP009615
If you want to access the data through queries such as a set of regions or annotation features instead of downloading the data at a project-level, we recommend using snapcount. It is an R/Bioconductor package for interfacing with Snaptron’s REST API. Here’s some example code you can use to get started with
## Install the snapcount R/Bioconductor package if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") ::install("snapcount") BiocManager ## Load snapcount R package library("snapcount") ## snapcount can be used with either a procedural interface query_jx(compilation = "gtex", regions = "CD99") query_jx(compilation = "gtex", regions = "CD99", range_filters = samples_count == 10) ## or using the query-builder class <- SnaptronQueryBuilder$new() sb $compilation("gtex")$regions("CD99")$query_jx()sb
recount3 files are hosted by IDIES and are publicly available. We separated every piece of information into its own file. These files can be accessed without using R through your own favorite programming solution. For example, the files for human study
SRP009615 annotated with GENCODE v26 are:
If you are interested in exploring what are the available projects in
recount3, you might be interested in accessing:
For more details about the structure of these files, check the Raw Files chapter.