pasilla

DOI: 10.18129/B9.bioc.pasilla    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see 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: 3.12

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 are provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181.

Author: Wolfgang Huber, Alejandro Reyes

Maintainer: Alejandro Reyes <alejandro.reyes.ds at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("pasilla")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("pasilla")

 

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

Details

biocViews	Drosophila_melanogaster_Data, ExperimentData, Genome, RNASeqData
Version	1.18.1
License	LGPL
Depends	R (>= 3.3.0)
Imports
LinkingTo
Suggests	DEXSeq, rmarkdown, BiocStyle, knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	blacksheepr
Suggests Me	BADER, DESeq, DESeq2, DEXSeq, EnhancedVolcano, IHWpaper, pasillaBamSubset, regionReport, ReportingTools, tidybulk
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	pasilla_1.18.1.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/pasilla
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/pasilla
Package Short Url	https://bioconductor.org/packages/pasilla/
Package Downloads Report	Download Stats