recount-package |
Explore and download data from the recount project. |
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 |