Explore and download data from the recount project

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Documentation for package ‘recount’ version 1.24.1

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abstract_search Search the abstracts from the SRA studies available via the recount project
add_metadata Add additional curated metadata to a recount rse object
add_predictions Add predicted phenotypes to a recount rse object
all_metadata This function downloads the metadata for all projects.
browse_study Open a SRA study id in the SRA website
coverage_matrix Given a set of regions for a chromosome, compute the coverage matrix for a given SRA study.
download_retry Retry multiple times to download a file
download_study Download data for a given SRA study id from the recount project
expressed_regions Identify expressed regions from the mean coverage for a given SRA project
find_geo Find the GEO accession id for a given SRA run
geo_characteristics Build a data.frame from GEO's charactersitics for a given sample
geo_info Extract information from GEO for a given sample
getRPKM Compute an RPKM matrix based on a RangedSummarizedExperiment object
getTPM Compute a TPM matrix based on a RangedSummarizedExperiment object
read_counts Compute read counts
recount_abstract Summary information at the project level for the recount project
recount_exons Exon annotation used in recount
recount_genes Gene annotation used in recount
recount_url Files and URLs hosted by the recount project
reproduce_ranges Reproduce the gene or exons used in the RangedSummarizedExperiment objects
rse_gene_SRP009615 RangedSummarizedExperiment at the gene level for study SRP009615
scale_counts Scale the raw counts provided by the recount project
snaptron_query Query Snaptron to get data from exon-exon junctions present in Intropolis