# Explore and download data from the recount project

## Documentation for package ‘recount’ version 1.18.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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