pasilla

This is the development version of pasilla; for the stable release version, see pasilla.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9

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 (3.24)

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>

Citation (from within R, enter citation("pasilla")):

Wolfgang Huber, Alejandro Reyes. 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. doi:10.18129/B9.bioc.pasilla, R package version 1.41.0, https://bioconductor.org/packages/pasilla.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Drosophila_melanogaster_Data, ExperimentData, Genome, RNASeqData
Version	1.41.0
In Bioconductor since	BioC 2.9 (R-2.14) (15 years)
License	LGPL
Depends	R (>= 3.5.0), DEXSeq
Imports
System Requirements
URL

Suggests	rmarkdown, BiocStyle, knitr, roxygen2
Linking To
Enhances
Depends On Me
Imports Me	blacksheepr
Suggests Me	BADER, DEXSeq, EnhancedVolcano, gsean, pasillaBamSubset, regionReport, ReportingTools, tidybulk, tidyprint
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	pasilla_1.41.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
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