CHANGES IN VERSION 1.0.17 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o recount_url now includes the URLs for the GTEx bigWig files. CHANGES IN VERSION 1.0.14 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o coverage_matrix() now returns a RangedSummarizedExperiment object. This matches the behavior of recount.bwtool::coverage_matrix_bwtool() and is more consistent with the use of RSE objects in recount. CHANGES IN VERSION 1.0.12 ------------------------- BUG FIXES o coverage_matrix()'s helper function .read_pheno() was failing for some projects. CHANGES IN VERSION 1.0.11 ------------------------- BUG FIXES o Fixed a bug in the counts in coverage_matrix(). They were being incorrectly multiplied by 100. CHANGES IN VERSION 1.0.8 ------------------------ SIGNIFICANT USER-VISIBLE CHANGES o The gene and exon counts are now based on Gencode v25 instead of UCSC knownGene hg38. CHANGES IN VERSION 1.0.7 ------------------------ BUG FIXES o Updated snaptron_query() to comply with recent changes in Snaptron. CHANGES IN VERSION 1.0.4 ------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Updated the package so you can now access TCGA data. Now there's over 8 terabytes of data available in the recount project! CHANGES IN VERSION 1.0.2 ------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Merged in changes from the devel branch (versions 1.1.1 and 1.1.2) to the release branch (v1.0.2) o snaptron_query() now can query GTEx and TCGA data. CHANGES IN VERSION 1.0.1 ------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Snaptron changed from stingray.cs.jhu.edu:8090 to snaptron.cs.jhu.edu so snaptron_query() has been changed accordingly. CHANGES IN VERSION 0.99.30 -------------------------- NEW FEATURES o Added the function snaptron_query() which queries Intropolis via Snaptron to find if an exon-exon junction is present in the data. CHANGES IN VERSION 0.99.29 -------------------------- BUF FIXES o Fixed an bug in the vignette. Thanks to Michael Love for noticing it! CHANGES IN VERSION 0.99.0 ------------------------- NEW FEATURES o Created the package skeleton for recount o Added the function reproduce_ranges() for re-creating the gene or exon level information used in the recount project. o Added the function abstract_search() for identifying SRA projects of interest by searching the abstracts. o Added the function browse_study() for opening a browser tab for further exploring a project. o Added the function download_study() for downloading the data from the recount project. o Added the function scale_counts() for properly scaling the counts before performing a differential expression analysis with the RangedSummarizedExperiment objects hosted in the recount project. o Added the function expressed_regions() for defining the expressed regions in a chromosome for a given SRA study. o Added the function coverage_matrix() for computing the coverage matrix based on the regions of interest for a given SRA study. o Added the function geo_info() for obtaining sample information from GEO. o Added the function find_geo() for finding the GEO accession id given a SRA run accession (id). This function will be useful for SRA projects that did not have GEO entries at the time recount's data was created. o Added the function geo_characteristics() for building a data.frame from geo_info()'s results for the characteristics. o Added the function all_metadata() which downloads all the phenotype data for all projects. This function can be useful for identifying projects and/or samples of interests.