pasilla

Data package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down by Brooks et al., Genome Research 2011.

Bioconductor version: Development (3.0)

This package provides per-exon and per-gene read counts computed for selected genes from RNA-seq data that were presented in the article "Conservation of an RNA regulatory map between Drosophila and mammals" by Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR, Genome Res. 2011 Feb;21(2):193-202, Epub 2010 Oct 4, PMID: 20921232. The experiment studied the effect of RNAi knockdown of Pasilla, the Drosophila melanogaster ortholog of mammalian NOVA1 and NOVA2, on the transcriptome. The package vignette describes how the data provided here were derived from the RNA-Seq read sequence data that is provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181

Author: Wolfgang Huber, Alejandro Reyes

Maintainer: Alejandro Reyes <reyes at embl.de>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("pasilla")

To cite this package in a publication, start R and enter:

    citation("pasilla")

Documentation

PDF R Script Data preprocessing and creation of the data objects pasillaGenes and pasillaExons
PDF   Reference Manual

Details

biocViews ExperimentData, RNAseqData
Version 0.5.0
License LGPL
Depends
Imports
Suggests locfit, edgeR, xtable, DEXSeq, DESeq
System Requirements
URL
Depends On Me
Imports Me
Suggests Me BADER, DESeq, DESeq2, DEXSeq, genefilter, GenomicRanges, pasillaBamSubset, ReportingTools

Package Downloads

Package Source pasilla_0.5.0.tar.gz
Windows Binary pasilla_0.5.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) pasilla_0.5.0.tgz
Mac OS X 10.9 (Mavericks) pasilla_0.5.0.tgz
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