NanoporeRNASeq

DOI: 10.18129/B9.bioc.NanoporeRNASeq    

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

Nanopore RNA-Seq Example data

Bioconductor version: 3.12

The NanoporeRNASeq package contains long read RNA-Seq data generated using Oxford Nanopore Sequencing. The data consists of 6 samples from two human cell lines (K562 and MCF7) that were generated by the SG-NEx project. Each of these cell lines has three replicates, with 1 direct RNA sequencing data and 2 cDNA sequencing data. Reads are aligned to chromosome 22 (Grch38) and stored as bam files. The original data is from the SG-NEx project.

Author: Jonathan Goeke Developer [aut], Ying Chen Developer [cre], Yuk Kei Wan Developer [aut]

Maintainer: Ying Chen Developer <chen_ying at gis.a-star.edu.sg>

Installation

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

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

BiocManager::install("NanoporeRNASeq")

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("NanoporeRNASeq")

 

HTML	R Script	NanoporeRNASeq
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	ExperimentData, ExperimentHub, Genome, RNASeqData, SequencingData
Version	1.0.0
License	GPL-3 + file LICENSE
Depends	R (>= 4.0.0), ExperimentHub(>= 1.15.3)
Imports
LinkingTo
Suggests	knitr, bambu, ggbio, BSgenome.Hsapiens.NCBI.GRCh38, circlize, ComplexHeatmap, apeglm, rlang, GenomicAlignments, Rsamtools
SystemRequirements
Enhances	parallel
URL	https://github.com/GoekeLab/NanoporeRNASeq
Depends On Me
Imports Me
Suggests Me	bambu
Links To Me
Build Report

Package Archives

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

Source Package	NanoporeRNASeq_1.0.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/NanoporeRNASeq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/NanoporeRNASeq
Package Short Url	https://bioconductor.org/packages/NanoporeRNASeq/
Package Downloads Report	Download Stats