Schurch16: Get the RNA-seq counts from Schurch et al. (2016)

In const-ae/HighlyReplicatedRNASeq: Collection of Bulk RNA-Seq Experiments With Many Replicates

Description

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.

Usage

Schurch16(hub = ExperimentHub())

Schurch16_metadata(hub = ExperimentHub())

Arguments

hub	an ExperimentHub object that is used to load the resource "EH3315" and "EH3316". Default: ExperimentHub()

Details

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.

Value

Schurch16()

returns a SummarizedExperiment with 7126 genes and 86 samples.

Schurch16_metadata()

returns a ExperimentHub object with the metadata on the Schurch16 dataset.

Author(s)

Constantin Ahlmann-Eltze

References

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

Examples

  Schurch16_metadata()

  se <- Schurch16()

  dim(se)
  colData(se)
  summary(c(assay(se, "counts")))

const-ae/HighlyReplicatedRNASeq documentation built on Jan. 19, 2021, 12:46 a.m.