#' #' #' A #' object with the counts stored in the assays slot. Set to #' `TRUE` if you want to match the defaults of. #' round If `TRUE`, the counts are rounded to integers. The scaling method is by #' AUC, as in the default option of. Set `scale` to #' `FALSE` if you want the raw coverage counts. #' scale If `TRUE`, the coverage counts will be scaled to read #' counts based on a library size of 40 million reads. #' verboseLoad If `TRUE` basic status updates for loading the data #' will be printed. #' bpparam A instance which #' will be used to calculate the coverage matrix in parallel.
Regions will be split into different chunks #' which can be useful when using a parallel instance as defined by #' `bpparam`. #' chunksize A single integer vector defining the chunksize to use for #' computing the coverage matrix. #' #' expressed_regions #' regions A object with regions #' for `chr` for which to calculate the coverage matrix.
#' #' Given a set of genomic regions as created by, this #' function computes the coverage matrix for a library size of 40 million 100 bp #' reads for a given SRA study. #' Given a set of regions for a chromosome, compute the coverage matrix for a #' given SRA study.
#Recount wowmatrix download
recount-package: recount: Explore and download data from the recount project.recount_genes: Gene annotation used in recount.recount_exons: Exon annotation used in recount.recount_abstract: Summary information at the project level for the recount.getTPM: Compute a TPM matrix based on a RangedSummarizedExperiment.getRPKM: Compute an RPKM matrix based on a RangedSummarizedExperiment.geo_info: Extract information from GEO for a given sample.geo_characteristics: Build a ame from GEO's charactersitics for a given.find_geo: Find the GEO accession id for a given SRA run.expressed_regions: Identify expressed regions from the mean coverage for a given.download_study: Download data for a given SRA study id from the recount.download_retry: Retry multiple times to download a file.coverage_matrix: Given a set of regions for a chromosome, compute the coverage.browse_study: Open a SRA study id in the SRA website.all_metadata: This function downloads the metadata for all projects.add_predictions: Add predicted phenotypes to a recount rse object.add_metadata: Add additional curated metadata to a recount rse object.abstract_search: Search the abstracts from the SRA studies available via the.You're MUCH better off using the curse client or the wowi minion. This of course means wowmatrix is forced to host anything their program offers on their own servers, which most addon author's refuse to even touch due to absolutely nothing in the way of revision control.
Lastly, there was the huge issue of the program leeching bandwidth off of wowi and curse without consent or even showing the other site's adds, both of which have since altered their download services to prevent wowmatrix (or any automated downloader) from functioning. It was also practically impossible to remove your addon from their service, and some author's had to resort to legal means to do so (issuing cease and desists to force them to remove the addon). To name a few, wowmatrix initially did not even cite the author's name for the addon a user was downloading, nor did it always have the most up-to-date version (causing a nightmare for bug reporting). End-User's found it convenient, but addon author's had A LOT off issues with it. I thought wowmatrix was not supported anymore?
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