Man pages for recount
Explore and download data from the recount project
| abstract_search | Search the abstracts from the SRA studies available via the... |
| 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... |
| download_retry | Retry multiple times to download a file |
| download_study | Download data for a given SRA study id from the recount... |
| expressed_regions | Identify expressed regions from the mean coverage for a given... |
| 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... |
| geo_info | Extract information from GEO for a given sample |
| getRPKM | Compute an RPKM matrix based on a RangedSummarizedExperiment... |
| getTPM | Compute a TPM matrix based on a RangedSummarizedExperiment... |
| read_counts | Compute read counts |
| recount_abstract | Summary information at the project level for the recount... |
| recount_exons | Exon annotation used in recount |
| recount_genes | Gene annotation used in recount |
| recount-package | recount: Explore and download data from the recount project |
| recount_url | Files and URLs hosted by the recount project |
| reproduce_ranges | Reproduce the gene or exons used in the... |
| rse_gene_SRP009615 | RangedSummarizedExperiment at the gene level for study... |
| scale_counts | Scale the raw counts provided by the recount project |
| snaptron_query | Query Snaptron to get data from exon-exon junctions present... |
