pasillaBamSubset

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see pasillaBamSubset.

Subset of BAM files from "Pasilla" experiment

Bioconductor version: 3.8

Subset of BAM files untreated1.bam (single-end reads) and untreated3.bam (paired-end reads) from "Pasilla" experiment (Pasilla knock-down by Brooks et al., Genome Research 2011). See the vignette in the pasilla data package for how BAM files untreated1.bam and untreated3.bam were obtained from the RNA-Seq read sequence data that is provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. Also contains the DNA sequence for fly chromosome 4 to which the reads can be mapped.

Author: Hervé Pagès

Maintainer: Hervé Pagès <hpages at fredhutch.org>

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

Installation

To install this package, start R (version "3.5") and enter:


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

BiocManager::install("pasillaBamSubset")

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

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNASeqData, ExperimentData, Genome, RNASeqData
Version	0.20.0
License	LGPL
Depends
Imports
System Requirements
URL

Suggests	pasilla
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	GenomicAlignments, GenomicFeatures, GenomicRanges, IRanges, karyoploteR, plyranges, TransView
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	pasillaBamSubset_0.20.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository	git clone https://git.bioconductor.org/packages/pasillaBamSubset
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/pasillaBamSubset
Package Short Url	https://bioconductor.org/packages/pasillaBamSubset/
Package Downloads Report	Download Stats