Baca: The Baca dataset

Description Usage Format Value Source References Examples

Description

The integrated Baca dataset contains the ExpressionSet Baca; its assayData contains deep sequenced RNA-Seq data of Bacillus anthracis under four stress conditions (with four replicates per stress conditions). The raw sequence reads derive from Passalacqua et al. (2012) and are availaible at Gene Expression Omnibus (GEO, accession number GSE36506). We have already mapped, counted and DESeq2 normalised these counts. The phenoData assigns the stress condition, i.e. ctrl, cold, salt and alcohol stress, to the samples. The featureData contains COG annotations of the genes.

Usage

1

Format

ExpressionSet

Value

ExpressionSet

Source

GEO GSE36506

References

Passalacqua, K. D., Varadarajan, A., Weist, C., Ondov, B. D., Byrd, B. et al. (2012) Strand-Specific RNA-Seq Reveals Ordered Patterns of Sense and Antisense Transcription in Bacillus anthracis. PLoS ONE, 7(8):e43350.

Examples

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data(Baca)
fData(Baca)
pData(Baca)
exprs(Baca)

covRNA documentation built on Nov. 1, 2018, 3:38 a.m.