| Title: | Collection of Bulk RNA-Seq Experiments With Many Replicates |
|---|---|
| Description: | Gene-level count matrix data for bulk RNA-seq dataset with many replicates. The data are provided as easy to use SummarizedExperiment objects. The source data that is made accessible through this package comes from https://github.com/bartongroup/profDGE48. |
| Authors: | Constantin Ahlmann-Eltze [aut, cre] (ORCID: <https://orcid.org/0000-0002-3762-068X>) |
| Maintainer: | Constantin Ahlmann-Eltze <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 1.25.0 |
| Built: | 2026-10-10 10:41:52 UTC |
| Source: | https://github.com/bioc/HighlyReplicatedRNASeq |
The HighlyReplicatedRNASeq package provides access to the count matrix results from studies with many replicates. These datasets can be valuable for benchmarking tools designed to handle RNA-seq data.
Available datasets:
Schurch et al. (2016): 86 samples of S. cerevisiae in two conditions
At the moment, this package contains only one dataset, but more datasets can be added in the future.
The data contains bulk RNA-seq count on 86 samples in two conditions. The first condition is wild type S. cerevisiae (taxonomic id: 1247190). The second condition is the same strain with a snf2 knockout.
Schurch16(hub = ExperimentHub()) Schurch16_metadata(hub = ExperimentHub())Schurch16(hub = ExperimentHub()) Schurch16_metadata(hub = ExperimentHub())
hub |
an ExperimentHub object that is used
to load the resource "EH3315" and "EH3316".
Default: |
Schurch et al. originally generated this dataset to benchmark RNA-seq differential expression tools and find out how many replicates are necessary to detect most differentially expressed genes. The data that is returned by this packge comes from the GitHub repository that accompanied the study.
Schurch16()returns a SummarizedExperiment with 7126 genes and 86 samples.
Schurch16_metadata()returns a ExperimentHub object with the metadata on the Schurch16 dataset.
Constantin Ahlmann-Eltze
Schurch, N. J., Schofield, P., Gierliński, M., Cole, C., Sherstnev, A., Singh, V., … Barton, G. J. (2016). How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? RNA, 22(6), 839–851. https://doi.org/10.1261/rna.053959.115
Schurch16_metadata() se <- Schurch16() dim(se) colData(se) summary(c(assay(se, "counts")))Schurch16_metadata() se <- Schurch16() dim(se) colData(se) summary(c(assay(se, "counts")))