stanfordData: Stanford RNA-Seq dataset

In aayushraman/DASC: Detecting hidden batch factors through data adaptive adjustment for biological effects

Stanford RNA-Seq dataset

Description

Stanford RNA-Seq dataset

Format

A list with two components.

Stanford gene expression dataset (Chen et. al. PNAS, 2015; Gilad et. al. F1000 Research, 2015). It is a filtered raw counts dataset which was published by Gilad et al. F1000 Research. 30 expression & mitochondrial genes were removed (Gilad et al.F1000 Research)

rawCounts

is a DataFrame object where each column represents a sample and each row represents a gene.

metadata

is a metadata information about each samples

Source

https://f1000research.com/articles/4-121/v1

References

1. Gilad Y and Mizrahi-Man O. A reanalysis of mouse ENCODE comparative gene expression data. F1000Research (2015)

2. in S, Lin Y, Nery JR, et al.: Comparison of the transcriptional landscapes between human and mouse tissues. Proc Natl Acad Sci USA (2014)

aayushraman/DASC documentation built on May 9, 2023, 12:03 a.m.