pasilla
This package is for version 3.15 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: 3.15
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("pasilla")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("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")| Data preprocessing and creation of the data objects pasillaGenes and pasillaExons | HTML | R Script |
| Reference Manual |
Details
| biocViews | Drosophila_melanogaster_Data, ExperimentData, Genome, RNASeqData |
| Version | 1.24.0 |
| License | LGPL |
| Depends | R (>= 3.5.0), DEXSeq |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | rmarkdown, BiocStyle, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | blacksheepr |
| Suggests Me | BADER, DESeq2, DEXSeq, EnhancedVolcano, pasillaBamSubset, regionReport, ReportingTools, tidybulk |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | pasilla_1.24.0.tar.gz |
| Windows Binary | |
| macOS Binary (x86_64) | |
| 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 |